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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_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘2.14.0’
* 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 ... OK
* 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                       90.244  2.514  96.635
PlotDimRed                        73.778  2.802  79.011
PlotOutliers                      38.020  0.967  40.427
PlotMarker                        32.535  1.373  34.637
UpdateMetaclusters                32.285  1.294  36.220
PlotStars                         27.320  1.142  29.571
GroupStats                        25.058  0.991  26.299
PlotGroups                        22.161  1.255  24.263
FlowSOM                           22.190  0.979  24.441
QueryMultiple                     17.162  0.578  19.766
AddAnnotation                     16.880  0.794  18.396
query_multiple                    17.009  0.511  18.360
Plot2DScatters                    15.579  0.999  16.798
PlotManualBars                    14.936  0.822  16.703
PlotNode                          13.298  0.874  14.394
GetFlowJoLabels                   13.523  0.615  14.716
QueryStarPlot                     12.763  0.454  14.072
PlotVariable                      12.334  0.783  15.190
PlotNumbers                       12.039  0.860  13.277
GetFeatures                       12.211  0.460  12.963
UpdateNodeSize                    12.192  0.267  13.421
PlotPies                          11.416  0.847  12.775
CountGroups                       11.464  0.583  12.964
PlotFlowSOM                       10.260  0.872  11.358
MetaclusterMFIs                   10.008  0.867  11.300
SaveClustersToFCS                  9.660  0.848  10.797
PlotLabels                         9.382  0.688  10.334
NClusters                          9.162  0.883  10.499
TestOutliers                       8.811  0.781  10.074
NMetaclusters                      8.642  0.821  10.075
FlowSOMSubset                      8.592  0.554   9.344
PlotOverview2D                     8.135  0.787   9.489
GetMetaclusters                    8.086  0.773   9.002
GetMFIs                            8.014  0.667   9.253
GetMetaclusterCVs                  7.907  0.739   8.818
MetaclusterCVs                     7.954  0.654   9.054
GetMetaclusterPercentagesPositive  7.775  0.777   8.660
GetPercentages                     7.731  0.782   8.619
print.FlowSOM                      7.715  0.792   8.603
GetMetaclusterMFIs                 7.899  0.602   8.929
GetClusterPercentagesPositive      7.529  0.675   8.355
GetCounts                          7.542  0.526   8.250
NewData                            7.367  0.658   8.543
GetClusters                        7.436  0.574   8.132
GetClusterMFIs                     7.488  0.459   8.477
ReadInput                          6.627  0.522   8.071
MetaClustering                     6.525  0.602   7.323
metaClustering_consensus           5.330  0.443   6.087
* 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-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** 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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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)