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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_2.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.16.0’
* 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 15.0.0 (clang-1500.0.40.1)’
* 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                       59.976  3.028  63.815
PlotDimRed                        52.778  3.839  57.381
PlotOutliers                      30.252  0.941  31.325
PlotMarker                        19.295  1.078  20.512
UpdateMetaclusters                17.266  1.370  18.779
PlotStars                         15.377  1.262  16.771
GroupStats                        14.232  1.051  15.434
FlowSOM                           13.521  1.525  15.541
PlotGroups                        12.371  0.977  13.460
Plot2DScatters                    10.659  0.798  11.593
query_multiple                    10.759  0.575  11.394
QueryMultiple                     10.778  0.546  11.339
PlotManualBars                     8.928  1.018  10.072
AddAnnotation                      9.192  0.612   9.840
GetFlowJoLabels                    8.542  0.547   9.149
PlotVariable                       7.824  1.189   9.095
PlotPies                           7.923  0.733   8.683
QueryStarPlot                      7.976  0.472   8.459
PlotNode                           7.383  0.687   8.099
CountGroups                        6.910  0.656   7.649
PlotNumbers                        6.544  0.679   7.302
PlotLabels                         6.123  0.903   7.144
MetaclusterMFIs                    5.774  1.185   7.077
SaveClustersToFCS                  6.105  0.807   7.006
PlotFlowSOM                        6.246  0.613   6.889
print.FlowSOM                      5.776  0.922   6.731
NClusters                          5.762  0.928   6.793
UpdateNodeSize                     6.329  0.261   6.615
PlotOverview2D                     5.975  0.596   6.603
GetFeatures                        5.981  0.484   6.515
NMetaclusters                      5.737  0.724   6.509
TestOutliers                       5.706  0.619   6.368
GetClusterPercentagesPositive      5.645  0.668   6.424
GetPercentages                     5.214  0.985   6.283
GetClusters                        5.185  0.735   6.118
GetMFIs                            5.160  0.716   5.939
GetMetaclusterMFIs                 5.127  0.577   5.728
MetaclusterCVs                     5.032  0.653   5.893
GetMetaclusters                    5.084  0.549   5.715
GetCounts                          5.088  0.533   5.767
GetMetaclusterPercentagesPositive  5.050  0.570   5.634
GetClusterMFIs                     4.922  0.635   5.619
GetMetaclusterCVs                  4.631  0.651   5.345
FlowSOMSubset                      4.759  0.493   5.336
* 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.

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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-arm64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.16.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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)