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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_2.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.12.0’
* 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                       98.524  2.496 117.572
PlotDimRed                        74.928  2.814  88.357
PlotOutliers                      40.618  0.794  47.808
PlotMarker                        36.711  1.259  44.480
UpdateMetaclusters                35.167  1.049  41.016
PlotStars                         30.525  0.909  35.510
GroupStats                        28.180  0.871  33.392
PlotGroups                        24.176  0.928  29.871
FlowSOM                           23.811  0.958  27.930
query_multiple                    19.718  0.481  23.174
QueryMultiple                     19.621  0.450  23.319
AddAnnotation                     18.418  0.676  23.055
Plot2DScatters                    16.838  0.673  20.421
PlotManualBars                    15.895  0.863  20.839
GetFlowJoLabels                   15.261  0.675  18.189
PlotNode                          14.097  0.648  18.125
QueryStarPlot                     14.297  0.345  16.494
PlotNumbers                       13.371  0.742  17.398
PlotVariable                      12.997  0.644  15.434
UpdateNodeSize                    13.318  0.253  14.617
GetFeatures                       12.734  0.356  14.748
PlotPies                          12.339  0.581  14.366
CountGroups                       11.691  0.492  13.823
SaveClustersToFCS                 10.573  0.716  12.838
PlotFlowSOM                       10.426  0.740  15.367
PlotLabels                        10.434  0.612  12.861
NClusters                          9.540  0.875  15.990
NMetaclusters                      9.546  0.791  13.541
MetaclusterMFIs                    9.532  0.627  11.485
TestOutliers                       9.299  0.539  11.441
MetaclusterCVs                     8.766  0.628  10.851
PlotOverview2D                     8.718  0.496  10.299
GetMetaclusterCVs                  8.392  0.706  10.587
FlowSOMSubset                      8.693  0.370  10.264
GetPercentages                     8.433  0.581  10.222
GetMetaclusterPercentagesPositive  8.372  0.583  10.172
print.FlowSOM                      8.301  0.599   9.805
GetMetaclusters                    8.275  0.582  10.032
GetMFIs                            8.216  0.610  10.033
GetMetaclusterMFIs                 8.245  0.556   9.718
GetClusters                        7.958  0.445   9.483
GetClusterPercentagesPositive      7.967  0.408   9.517
GetClusterMFIs                     7.898  0.466   9.526
GetCounts                          7.947  0.407   9.344
NewData                            7.824  0.525  11.411
MetaClustering                     7.081  0.519   9.418
ReadInput                          6.943  0.411   8.222
metaClustering_consensus           5.899  0.454   6.958
PlotSD                             4.881  0.130   5.519
* 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-3.19-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)