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### Running command:
###
###   /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_2.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘2.17.0’
* 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                       51.983  3.196  62.287
PlotDimRed                        44.187  3.461  51.850
PlotOutliers                      35.511  1.502  39.481
UpdateMetaclusters                18.854  1.619  21.101
PlotMarker                        17.056  1.626  23.571
PlotStars                         16.567  1.232  18.287
GroupStats                        13.646  1.351  16.371
PlotGroups                        13.544  1.227  14.987
FlowSOM                           12.444  1.562  15.438
Plot2DScatters                    10.854  1.082  12.666
PlotManualBars                     9.882  1.309  12.878
query_multiple                    10.427  0.656  12.707
QueryMultiple                     10.078  0.722  14.356
AddAnnotation                      9.606  0.917  12.237
GetFlowJoLabels                    8.076  0.978   9.445
PlotNumbers                        7.825  1.020   9.772
PlotNode                           7.335  1.135  11.131
PlotVariable                       7.226  1.189  10.700
PlotPies                           6.683  1.233  12.585
QueryStarPlot                      7.209  0.484   9.508
UpdateNodeSize                     7.264  0.326   7.708
SaveClustersToFCS                  5.588  1.338   9.175
GetFeatures                        6.135  0.695   7.556
PlotFlowSOM                        5.891  0.874   6.862
PlotLabels                         5.887  0.876   7.752
NMetaclusters                      5.555  1.073   8.258
CountGroups                        5.762  0.821   8.252
PlotOverview2D                     5.316  0.929   7.001
TestOutliers                       4.944  1.234   7.387
MetaclusterMFIs                    4.769  1.303  10.249
NClusters                          4.910  1.161   9.994
GetMFIs                            4.708  1.252   9.092
GetMetaclusterCVs                  4.564  1.195   6.671
GetMetaclusters                    4.808  0.933   6.029
GetMetaclusterMFIs                 4.765  0.865   5.732
GetPercentages                     4.790  0.825   5.768
GetMetaclusterPercentagesPositive  4.703  0.871   5.717
print.FlowSOM                      4.507  1.033   5.673
MetaclusterCVs                     4.218  1.091   7.191
GetCounts                          4.527  0.754   5.535
GetClusters                        4.213  0.801   5.474
GetClusterMFIs                     4.237  0.761   7.405
FlowSOMSubset                      4.011  0.806   7.940
MetaClustering                     3.669  0.947   5.564
GetClusterPercentagesPositive      3.695  0.825   7.403
NewData                            3.769  0.688   5.406
ReadInput                          3.021  1.148   8.840
* 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 ‘2.17.0’
** 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)