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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 Patched (2025-11-05 r88990)
* 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                       99.218  2.299 108.811
PlotDimRed                        74.437  2.627  81.484
PlotOutliers                      70.251  1.330  78.649
PlotMarker                        37.274  1.183  40.287
UpdateMetaclusters                35.336  1.496  39.940
PlotStars                         30.561  1.152  34.395
GroupStats                        27.809  0.856  30.574
FlowSOM                           23.400  1.064  25.789
PlotGroups                        23.434  1.017  25.559
Plot2DScatters                    21.326  0.747  23.881
QueryMultiple                     20.778  0.536  23.513
query_multiple                    20.575  0.583  22.276
AddAnnotation                     17.967  0.739  20.106
PlotManualBars                    17.422  0.938  19.277
QueryStarPlot                     14.807  0.353  16.239
GetFlowJoLabels                   14.045  0.645  15.054
PlotNode                          13.599  0.770  15.276
UpdateNodeSize                    13.400  0.283  14.374
PlotNumbers                       13.005  0.661  14.440
PlotVariable                      12.688  0.762  15.406
PlotPies                          12.348  0.818  13.701
GetFeatures                       11.898  0.357  13.208
PlotFlowSOM                       11.383  0.744  13.013
CountGroups                       11.496  0.627  12.538
SaveClustersToFCS                  9.757  0.849  11.128
PlotLabels                         9.716  0.691  10.572
MetaclusterMFIs                    9.279  0.886  10.863
NMetaclusters                      9.399  0.748  10.784
NClusters                          8.791  0.769  10.031
TestOutliers                       8.857  0.681  10.193
PlotOverview2D                     8.651  0.562   9.782
GetMetaclusterPercentagesPositive  8.496  0.630   9.537
MetaclusterCVs                     8.119  0.811   9.232
FlowSOMSubset                      8.480  0.412   9.845
GetPercentages                     8.272  0.576  10.106
print.FlowSOM                      8.009  0.749   9.049
GetMetaclusterCVs                  7.968  0.776   9.012
GetMFIs                            8.039  0.643   9.242
GetMetaclusters                    8.056  0.583   9.241
GetMetaclusterMFIs                 8.011  0.516   8.961
GetClusters                        7.849  0.402   9.036
GetClusterPercentagesPositive      7.811  0.411   8.952
GetClusterMFIs                     7.755  0.407   8.720
GetCounts                          7.713  0.409   8.625
NewData                            7.608  0.501   9.188
ReadInput                          6.508  0.618   7.445
MetaClustering                     6.519  0.489   7.358
metaClustering_consensus           5.099  0.555   5.743
* 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)