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### Running command:
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###   /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                       98.552  2.790 105.691
PlotDimRed                        73.145  2.715  79.127
PlotOutliers                      68.435  1.255  71.431
PlotMarker                        37.502  1.628  41.790
UpdateMetaclusters                34.965  1.400  38.337
PlotStars                         30.244  1.386  32.052
GroupStats                        27.225  1.030  29.181
FlowSOM                           23.346  1.568  25.201
PlotGroups                        23.274  1.416  25.467
Plot2DScatters                    20.796  1.088  22.168
QueryMultiple                     20.641  0.564  21.853
query_multiple                    19.892  0.491  20.516
AddAnnotation                     17.765  0.952  19.150
PlotManualBars                    17.342  1.046  19.213
QueryStarPlot                     15.085  0.488  16.849
GetFlowJoLabels                   13.968  0.809  15.165
PlotNode                          13.698  1.061  15.825
PlotNumbers                       13.448  0.832  16.239
UpdateNodeSize                    13.655  0.235  14.762
PlotVariable                      12.651  0.886  14.011
PlotPies                          12.410  1.054  13.722
PlotFlowSOM                       11.294  1.263  12.657
CountGroups                       11.416  0.827  12.381
GetFeatures                       11.542  0.423  12.010
PlotLabels                        10.449  0.821  12.133
SaveClustersToFCS                  9.767  0.925  11.551
NClusters                          9.136  1.263  10.506
NMetaclusters                      9.064  1.326  10.501
MetaclusterMFIs                    9.202  1.011  10.880
TestOutliers                       8.799  0.695  10.169
PlotOverview2D                     8.642  0.805   9.643
print.FlowSOM                      7.956  0.976   9.136
GetMFIs                            8.049  0.837   9.156
GetMetaclusterPercentagesPositive  7.923  0.954   9.072
MetaclusterCVs                     7.990  0.882   9.140
FlowSOMSubset                      8.326  0.487   9.555
GetPercentages                     7.974  0.829   9.038
GetMetaclusterMFIs                 7.912  0.861   9.069
GetClusterPercentagesPositive      8.050  0.693   8.814
GetMetaclusters                    7.878  0.733   9.127
GetMetaclusterCVs                  7.955  0.636   9.025
GetCounts                          7.697  0.806   8.686
GetClusters                        7.612  0.722   8.439
GetClusterMFIs                     7.691  0.598   8.448
NewData                            7.322  0.703   8.190
ReadInput                          6.530  0.564   7.529
MetaClustering                     6.330  0.595   7.303
metaClustering_consensus           5.226  0.415   6.056
* 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:
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###   /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)