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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 4.4.2 (2024-10-31)
* 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                       91.219  2.512 101.370
PlotDimRed                        74.638  2.859  82.392
PlotOutliers                      38.735  0.838  42.520
PlotMarker                        33.274  1.245  36.751
UpdateMetaclusters                32.795  1.213  37.174
PlotStars                         28.733  1.120  33.941
GroupStats                        26.384  1.013  29.683
PlotGroups                        22.916  1.179  26.542
FlowSOM                           22.647  1.104  25.025
query_multiple                    17.590  0.580  19.303
AddAnnotation                     17.229  0.746  19.489
QueryMultiple                     17.246  0.496  18.537
Plot2DScatters                    16.041  0.721  17.953
PlotManualBars                    14.913  0.792  16.798
GetFlowJoLabels                   13.761  0.613  15.528
PlotNode                          13.068  0.738  14.841
PlotNumbers                       12.411  0.700  14.537
QueryStarPlot                     12.694  0.382  13.595
PlotVariable                      12.229  0.746  14.874
GetFeatures                       12.425  0.420  13.556
UpdateNodeSize                    12.211  0.271  13.265
PlotPies                          11.673  0.705  13.030
CountGroups                       11.125  0.632  12.388
PlotFlowSOM                       10.838  0.652  12.853
SaveClustersToFCS                  9.823  0.677  11.084
MetaclusterMFIs                    9.321  0.760  10.703
PlotLabels                         9.487  0.548  10.754
NMetaclusters                      9.204  0.744  13.678
NClusters                          9.254  0.639  10.734
TestOutliers                       8.933  0.590  10.690
FlowSOMSubset                      8.708  0.414   9.558
GetPercentages                     8.189  0.603   8.953
PlotOverview2D                     8.182  0.559   9.258
MetaclusterCVs                     8.056  0.617   9.571
GetMFIs                            7.991  0.664   9.183
GetMetaclusterCVs                  7.974  0.621   9.112
print.FlowSOM                      7.911  0.668   9.005
GetMetaclusters                    7.931  0.607   8.900
GetMetaclusterMFIs                 7.906  0.621   8.986
GetMetaclusterPercentagesPositive  7.905  0.540   9.088
GetCounts                          7.687  0.465   8.945
GetClusterPercentagesPositive      7.596  0.482   8.545
GetClusterMFIs                     7.611  0.447   8.592
GetClusters                        7.568  0.445   8.407
NewData                            7.479  0.501   8.910
ReadInput                          6.809  0.504   7.859
MetaClustering                     6.626  0.527   7.672
metaClustering_consensus           5.371  0.338   5.981
* 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)