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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 4.4.1 (2024-06-14)
* 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 12.7.5
* 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                       92.968  2.661 114.134
PlotDimRed                        75.816  2.546  92.268
PlotOutliers                      39.208  0.876  45.697
PlotMarker                        33.833  1.186  40.291
UpdateMetaclusters                32.323  1.109  37.815
PlotStars                         28.398  1.037  33.237
GroupStats                        26.744  0.900  32.723
FlowSOM                           22.857  0.897  28.262
PlotGroups                        22.373  1.042  26.825
QueryMultiple                     17.505  0.513  19.912
query_multiple                    17.470  0.528  21.113
AddAnnotation                     17.317  0.667  21.576
Plot2DScatters                    16.299  0.600  20.150
PlotManualBars                    15.084  0.576  17.881
GetFlowJoLabels                   13.830  0.661  16.744
PlotNode                          13.087  0.631  15.484
QueryStarPlot                     13.096  0.371  15.428
PlotNumbers                       12.569  0.665  15.004
GetFeatures                       12.485  0.394  14.900
PlotVariable                      12.150  0.627  14.116
UpdateNodeSize                    12.383  0.254  13.620
PlotPies                          11.835  0.630  14.713
CountGroups                       11.335  0.544  13.331
PlotFlowSOM                       10.545  0.758  12.948
SaveClustersToFCS                  9.881  0.690  12.498
PlotLabels                         9.977  0.591  11.913
NMetaclusters                      9.374  0.617  12.087
NClusters                          9.320  0.657  12.411
MetaclusterMFIs                    9.250  0.621  11.628
TestOutliers                       9.286  0.534  11.424
FlowSOMSubset                      8.885  0.407  10.841
PlotOverview2D                     8.515  0.575  11.644
GetPercentages                     8.484  0.538  10.838
GetMetaclusterMFIs                 8.422  0.549  10.713
print.FlowSOM                      8.143  0.630  10.599
GetMetaclusters                    8.069  0.674  10.323
GetMFIs                            8.033  0.646  10.067
MetaclusterCVs                     8.080  0.599  10.275
GetMetaclusterCVs                  8.154  0.523  10.091
GetMetaclusterPercentagesPositive  8.113  0.534  10.231
NewData                            7.965  0.499  10.207
GetClusterPercentagesPositive      7.759  0.464   9.855
GetClusterMFIs                     7.757  0.458   9.831
GetCounts                          7.725  0.448  10.025
GetClusters                        7.684  0.454   9.520
ReadInput                          6.780  0.486   8.210
MetaClustering                     6.569  0.520   8.232
metaClustering_consensus           5.405  0.331   6.841
PlotSD                             4.250  0.102   5.452
* 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)