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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 12.7.6
* 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                       93.485  2.565 115.374
PlotDimRed                        75.493  2.595  89.771
PlotOutliers                      39.153  0.787  47.373
PlotMarker                        33.253  1.096  39.258
UpdateMetaclusters                33.069  1.185  40.804
PlotStars                         28.471  0.920  33.096
GroupStats                        26.547  0.879  32.121
FlowSOM                           23.185  0.969  28.880
PlotGroups                        22.550  0.905  26.603
AddAnnotation                     17.336  0.700  22.200
QueryMultiple                     17.511  0.432  20.343
query_multiple                    17.366  0.494  20.279
Plot2DScatters                    16.318  0.639  19.658
PlotManualBars                    15.078  0.661  18.344
GetFlowJoLabels                   13.873  0.664  16.969
PlotNode                          12.995  0.612  15.432
PlotNumbers                       12.665  0.594  15.070
QueryStarPlot                     12.727  0.308  14.652
UpdateNodeSize                    12.629  0.269  15.815
PlotVariable                      12.247  0.645  14.770
GetFeatures                       12.362  0.388  14.841
PlotPies                          11.675  0.615  13.641
CountGroups                       11.427  0.580  14.960
PlotFlowSOM                       10.462  0.688  12.735
MetaclusterMFIs                    9.928  0.698  12.717
SaveClustersToFCS                  9.809  0.592  11.391
PlotLabels                         9.614  0.555  11.601
NMetaclusters                      9.227  0.660  11.667
NClusters                          9.285  0.570  12.445
TestOutliers                       9.052  0.564  10.905
GetMetaclusterPercentagesPositive  8.700  0.596  11.065
FlowSOMSubset                      8.758  0.378  10.710
MetaclusterCVs                     8.535  0.589  11.105
GetMetaclusterCVs                  8.480  0.538  10.928
GetMFIs                            8.404  0.582  10.636
PlotOverview2D                     8.335  0.520  10.753
GetMetaclusters                    8.026  0.539  10.418
print.FlowSOM                      7.999  0.552  10.015
GetPercentages                     8.010  0.540   9.931
GetMetaclusterMFIs                 7.996  0.519  10.086
GetClusterMFIs                     7.937  0.516  10.190
GetClusterPercentagesPositive      7.656  0.444   9.464
GetCounts                          7.669  0.410   9.407
GetClusters                        7.605  0.439   9.402
NewData                            7.527  0.406   9.230
ReadInput                          6.690  0.454   7.950
MetaClustering                     6.562  0.433   8.241
metaClustering_consensus           5.319  0.367   6.705
PlotSD                             4.630  0.228   5.409
* 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)