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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_2.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.19.0’
* 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 14.0.3 (clang-1403.0.22.14.1)’
* 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 ... INFO
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                       52.540  2.290  54.993
PlotDimRed                        38.787  2.282  41.543
PlotOutliers                      36.527  1.070  38.072
PlotMarker                        20.493  1.249  22.039
UpdateMetaclusters                17.878  1.300  19.386
PlotStars                         16.816  1.155  18.250
GroupStats                        13.998  0.839  14.979
FlowSOM                           13.066  1.022  14.206
PlotGroups                        12.219  1.068  13.402
QueryMultiple                     10.985  0.639  11.901
query_multiple                    11.037  0.478  11.760
Plot2DScatters                    10.312  0.618  11.032
AddAnnotation                      9.663  0.657  10.406
PlotManualBars                     9.129  0.844  10.122
GetFlowJoLabels                    7.878  0.670   8.642
PlotVariable                       7.413  1.065   8.806
QueryStarPlot                      7.828  0.382   8.317
PlotNode                           7.429  0.627   8.159
PlotPies                           7.220  0.761   8.099
PlotNumbers                        7.219  0.731   8.061
UpdateNodeSize                     6.706  0.282   7.069
CountGroups                        6.326  0.587   6.983
PlotFlowSOM                        6.143  0.743   6.971
PlotLabels                         5.731  0.693   6.505
SaveClustersToFCS                  5.533  0.766   6.391
MetaclusterMFIs                    5.383  0.798   6.249
GetFeatures                        5.649  0.435   6.143
PlotOverview2D                     5.385  0.584   6.054
TestOutliers                       5.155  0.764   6.000
NClusters                          5.221  0.689   5.969
NMetaclusters                      5.181  0.727   5.991
GetMetaclusterCVs                  4.807  0.722   5.597
GetMetaclusterPercentagesPositive  4.870  0.606   5.538
MetaclusterCVs                     4.786  0.640   5.481
print.FlowSOM                      4.657  0.713   5.447
GetMetaclusterMFIs                 4.757  0.605   5.426
GetMFIs                            4.620  0.682   5.376
GetMetaclusters                    4.644  0.643   5.353
GetCounts                          4.789  0.492   5.337
GetPercentages                     4.649  0.618   5.338
GetClusterMFIs                     4.544  0.514   5.112
NewData                            4.508  0.504   5.077
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-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/4.6-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.19.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
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/4.6-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)