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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                       99.608  2.410 116.730
PlotDimRed                        74.329  2.419  85.551
PlotOutliers                      70.219  1.203  79.634
PlotMarker                        37.345  1.022  41.457
UpdateMetaclusters                35.006  1.078  40.103
PlotStars                         30.437  1.118  36.134
GroupStats                        27.481  0.866  31.216
PlotGroups                        23.483  0.909  27.095
FlowSOM                           23.261  0.887  26.583
Plot2DScatters                    21.167  0.717  24.267
QueryMultiple                     20.794  0.451  24.231
query_multiple                    20.449  0.505  22.686
AddAnnotation                     18.044  0.683  21.076
PlotManualBars                    17.357  0.612  20.260
QueryStarPlot                     15.010  0.468  18.286
GetFlowJoLabels                   14.349  0.692  16.257
PlotNode                          13.812  0.623  15.696
UpdateNodeSize                    13.639  0.346  15.627
PlotNumbers                       13.399  0.582  16.922
PlotVariable                      12.829  0.647  16.188
PlotPies                          12.673  0.759  16.362
GetFeatures                       11.962  0.353  13.143
CountGroups                       11.548  0.515  13.176
PlotFlowSOM                       10.801  0.624  12.322
PlotLabels                        10.287  0.550  12.469
SaveClustersToFCS                  9.842  0.718  12.621
NMetaclusters                      9.227  0.739  11.251
MetaclusterMFIs                    9.234  0.681  10.750
NClusters                          9.188  0.684  10.931
TestOutliers                       8.862  0.467  10.699
PlotOverview2D                     8.695  0.579  10.395
FlowSOMSubset                      8.378  0.379   9.743
GetPercentages                     8.069  0.630   9.695
MetaclusterCVs                     8.105  0.583   9.611
GetMFIs                            8.103  0.582   9.860
GetMetaclusterPercentagesPositive  8.061  0.570  10.067
GetMetaclusterCVs                  8.102  0.526   9.889
print.FlowSOM                      7.978  0.637   9.493
GetClusterMFIs                     8.043  0.432   9.458
GetMetaclusterMFIs                 7.927  0.523   9.374
GetMetaclusters                    7.940  0.506   9.305
GetCounts                          7.692  0.400   8.823
GetClusterPercentagesPositive      7.676  0.370   8.767
GetClusters                        7.675  0.370   8.805
MetaClustering                     7.285  0.625   8.887
NewData                            7.385  0.445   8.651
ReadInput                          6.702  0.533   8.385
metaClustering_consensus           5.140  0.381   5.949
PlotSD                             4.425  0.208   5.199
* 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)