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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 RC (2025-06-05 r88288)
* 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 ‘2.16.0’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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                       98.826  2.450 104.580
PlotDimRed                        74.778  2.852  79.448
PlotOutliers                      69.438  1.238  72.276
PlotMarker                        37.113  1.343  39.814
UpdateMetaclusters                34.024  1.473  36.120
PlotStars                         30.264  1.290  35.373
GroupStats                        26.833  1.423  28.402
FlowSOM                           23.337  1.469  25.575
PlotGroups                        23.294  1.281  24.814
Plot2DScatters                    20.998  0.873  22.858
query_multiple                    21.054  0.656  22.498
QueryMultiple                     20.363  0.490  21.763
AddAnnotation                     17.768  0.987  19.294
PlotManualBars                    17.585  1.090  19.190
QueryStarPlot                     14.621  0.406  15.489
GetFlowJoLabels                   14.004  0.978  15.126
PlotNode                          13.485  0.831  14.984
PlotVariable                      12.703  1.036  15.658
PlotNumbers                       12.754  0.969  13.874
UpdateNodeSize                    13.417  0.270  14.026
PlotPies                          12.379  0.928  13.520
GetFeatures                       11.671  0.577  12.470
CountGroups                       11.399  0.792  12.377
PlotFlowSOM                       10.784  1.261  12.553
SaveClustersToFCS                 10.166  1.054  11.741
PlotLabels                         9.915  0.846  11.231
MetaclusterMFIs                    9.310  1.088  11.267
NClusters                          9.259  1.107  10.726
NMetaclusters                      9.304  0.802  10.627
TestOutliers                       8.944  0.838   9.959
FlowSOMSubset                      8.730  0.575   9.636
GetPercentages                     8.436  0.855   9.665
GetMetaclusters                    8.396  0.845   9.464
PlotOverview2D                     8.525  0.696   9.451
MetaclusterCVs                     8.025  1.101   9.196
GetMFIs                            7.989  0.927   8.998
GetMetaclusterPercentagesPositive  7.995  0.817   9.233
GetMetaclusterCVs                  7.995  0.815   9.118
GetMetaclusterMFIs                 8.106  0.616   9.287
print.FlowSOM                      7.798  0.858   8.746
GetCounts                          7.702  0.703   8.471
GetClusterMFIs                     7.571  0.762   8.404
GetClusters                        7.647  0.616   8.389
GetClusterPercentagesPositive      7.643  0.612   8.531
NewData                            7.439  0.652   8.537
ReadInput                          6.464  0.726   7.454
MetaClustering                     6.363  0.755   7.187
metaClustering_consensus           5.216  0.483   5.876
* 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-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.16.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.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)