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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                       99.001  2.157 113.308
PlotDimRed                        74.487  2.439  84.682
PlotOutliers                      70.296  0.978  81.053
PlotMarker                        37.315  0.955  43.109
UpdateMetaclusters                35.170  1.098  42.344
PlotStars                         30.696  1.108  36.177
GroupStats                        27.566  0.725  31.659
FlowSOM                           23.400  0.886  26.825
PlotGroups                        23.311  0.843  26.404
Plot2DScatters                    21.500  0.675  24.633
QueryMultiple                     21.187  0.692  25.821
query_multiple                    21.017  0.558  24.951
AddAnnotation                     17.977  0.690  21.363
PlotManualBars                    17.342  0.718  19.960
QueryStarPlot                     14.938  0.340  16.903
PlotNode                          14.308  0.671  16.787
GetFlowJoLabels                   14.213  0.582  16.085
UpdateNodeSize                    13.501  0.255  15.573
PlotNumbers                       13.059  0.551  14.701
PlotVariable                      12.800  0.646  15.372
PlotPies                          11.957  0.796  16.773
GetFeatures                       12.100  0.360  13.729
CountGroups                       11.471  0.489  13.018
PlotFlowSOM                       10.775  0.593  12.671
SaveClustersToFCS                  9.740  0.683  11.737
PlotLabels                         9.824  0.529  11.736
NMetaclusters                      9.258  0.628  10.810
NClusters                          9.245  0.631  11.234
MetaclusterMFIs                    9.220  0.640  10.798
TestOutliers                       9.044  0.552  11.050
PlotOverview2D                     8.506  0.732  11.931
GetMFIs                            8.563  0.612   9.926
print.FlowSOM                      8.458  0.685  10.351
FlowSOMSubset                      8.450  0.372   9.820
MetaclusterCVs                     8.084  0.555   9.678
GetPercentages                     8.056  0.565   9.928
GetMetaclusterMFIs                 8.004  0.530   9.073
GetMetaclusters                    7.997  0.523   9.709
GetMetaclusterCVs                  8.011  0.504   9.011
GetMetaclusterPercentagesPositive  7.958  0.508   9.273
GetCounts                          7.798  0.394   9.158
GetClusterPercentagesPositive      7.781  0.376   9.480
GetClusters                        7.752  0.363   9.300
GetClusterMFIs                     7.728  0.365   8.950
NewData                            7.631  0.444   8.936
ReadInput                          7.431  0.638   9.018
MetaClustering                     6.397  0.456   7.579
metaClustering_consensus           5.181  0.278   6.122
* 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)