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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                       90.854  2.658  98.297
PlotDimRed                        73.533  2.772  78.806
PlotOutliers                      38.176  1.072  40.608
PlotMarker                        32.586  1.521  35.006
UpdateMetaclusters                32.347  1.332  36.010
PlotStars                         28.043  1.248  31.709
GroupStats                        26.002  1.046  28.592
PlotGroups                        22.317  1.328  24.714
FlowSOM                           22.059  1.351  24.031
AddAnnotation                     16.968  0.820  18.557
QueryMultiple                     17.050  0.531  18.274
query_multiple                    16.881  0.555  17.764
Plot2DScatters                    15.959  1.092  17.346
PlotManualBars                    14.789  0.795  16.330
GetFlowJoLabels                   13.634  0.708  16.289
PlotNode                          12.646  0.809  13.638
QueryStarPlot                     12.913  0.390  13.433
PlotVariable                      12.404  0.876  14.542
PlotNumbers                       12.232  0.775  13.634
GetFeatures                       12.311  0.373  13.725
UpdateNodeSize                    11.891  0.253  12.280
PlotPies                          11.374  0.687  12.307
CountGroups                       11.071  0.770  12.085
PlotFlowSOM                       10.268  0.915  11.353
SaveClustersToFCS                  9.681  0.781  10.921
PlotLabels                         9.600  0.740  10.803
NMetaclusters                      9.138  1.083  10.331
MetaclusterMFIs                    9.176  0.795  10.391
NClusters                          9.017  0.944  10.100
TestOutliers                       8.686  0.641   9.500
GetMetaclusterPercentagesPositive  8.064  0.885   9.032
FlowSOMSubset                      8.379  0.514   9.517
PlotOverview2D                     8.017  0.725   8.945
GetMetaclusterCVs                  7.840  0.827   8.759
GetMFIs                            7.817  0.846   8.872
GetPercentages                     7.823  0.837   8.819
GetMetaclusterMFIs                 7.872  0.783   8.736
MetaclusterCVs                     7.933  0.660   8.846
print.FlowSOM                      7.730  0.790   8.701
GetMetaclusters                    7.828  0.679   8.660
GetCounts                          7.631  0.641   8.467
NewData                            7.330  0.785   8.182
GetClusterPercentagesPositive      7.541  0.524   8.543
GetClusters                        7.459  0.575   8.350
GetClusterMFIs                     7.466  0.527   8.272
ReadInput                          6.708  0.519   7.484
MetaClustering                     6.489  0.483   7.380
metaClustering_consensus           5.661  0.553   6.506
* 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)