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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                       53.073  2.326  55.638
PlotDimRed                        39.404  2.497  42.550
PlotOutliers                      35.906  0.963  37.329
PlotMarker                        19.929  1.142  21.373
UpdateMetaclusters                18.034  1.198  19.478
PlotStars                         17.191  1.172  18.645
GroupStats                        14.049  0.820  14.992
FlowSOM                           13.040  1.041  14.212
PlotGroups                        12.456  1.039  13.648
query_multiple                    11.185  0.506  11.888
QueryMultiple                     11.008  0.579  11.742
Plot2DScatters                    10.407  0.710  11.236
AddAnnotation                      9.460  0.638  10.186
PlotManualBars                     9.119  0.784  10.051
PlotPies                           7.954  0.744   8.835
PlotNode                           7.938  0.737   8.789
GetFlowJoLabels                    8.023  0.636   8.735
QueryStarPlot                      7.849  0.314   8.270
PlotVariable                       7.334  0.789   8.311
PlotNumbers                        7.322  0.790   8.218
PlotFlowSOM                        6.912  0.708   7.695
UpdateNodeSize                     6.728  0.229   7.076
CountGroups                        6.363  0.586   7.059
PlotLabels                         5.784  0.659   6.548
SaveClustersToFCS                  5.386  0.780   6.283
NClusters                          5.252  0.844   6.240
GetFeatures                        5.700  0.372   6.130
PlotOverview2D                     5.407  0.528   6.022
MetaclusterMFIs                    5.100  0.725   5.889
NMetaclusters                      5.081  0.724   5.884
MetaclusterCVs                     4.868  0.788   5.815
TestOutliers                       4.938  0.707   5.728
GetMetaclusterCVs                  4.774  0.637   5.492
GetMetaclusterPercentagesPositive  4.723  0.631   5.412
GetPercentages                     4.730  0.624   5.424
print.FlowSOM                      4.622  0.659   5.468
GetMetaclusters                    4.646  0.613   5.319
GetMFIs                            4.641  0.603   5.300
GetMetaclusterMFIs                 4.631  0.586   5.265
GetCounts                          4.514  0.625   5.204
* 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)