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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_2.14.0.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: aarch64-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 Ventura 13.7.1
* 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 15.0.0 (clang-1500.0.40.1)’
* 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                       58.019  2.694  60.969
PlotDimRed                        50.272  2.253  52.889
PlotMarker                        16.660  1.318  18.027
UpdateMetaclusters                16.172  1.192  17.443
PlotOutliers                      16.220  0.802  17.082
FlowSOM                           12.742  1.112  14.080
PlotStars                         12.770  0.957  13.760
GroupStats                        12.481  0.850  13.363
PlotGroups                        10.973  0.983  11.975
AddAnnotation                      9.174  0.610   9.810
query_multiple                     8.882  0.509   9.396
QueryMultiple                      8.477  0.508   9.042
Plot2DScatters                     8.124  0.611   8.761
GetFlowJoLabels                    7.851  0.705   8.605
PlotManualBars                     7.362  0.696   8.080
PlotVariable                       7.220  0.694   8.006
PlotNode                           6.807  0.678   7.505
QueryStarPlot                      6.852  0.466   7.324
PlotPies                           6.351  0.739   7.110
SaveClustersToFCS                  6.326  0.757   7.095
PlotFlowSOM                        6.304  0.721   7.043
CountGroups                        6.278  0.658   6.951
PlotNumbers                        6.009  0.664   6.750
NMetaclusters                      5.479  0.738   6.253
PlotLabels                         5.537  0.620   6.176
MetaclusterMFIs                    5.447  0.692   6.172
PlotOverview2D                     5.391  0.557   5.963
UpdateNodeSize                     5.634  0.247   5.906
NClusters                          5.138  0.725   5.887
TestOutliers                       5.254  0.580   5.843
print.FlowSOM                      4.954  0.826   5.865
GetMetaclusterPercentagesPositive  4.903  0.658   5.575
GetMetaclusterCVs                  4.831  0.697   5.542
MetaclusterCVs                     4.949  0.566   5.537
GetMFIs                            4.894  0.600   5.515
GetMetaclusterMFIs                 4.850  0.618   5.479
GetClusterPercentagesPositive      4.866  0.599   5.473
GetMetaclusters                    4.856  0.594   5.534
GetPercentages                     4.772  0.589   5.394
FlowSOMSubset                      4.757  0.483   5.328
GetFeatures                        4.759  0.419   5.234
GetClusterMFIs                     4.526  0.633   5.168
GetClusters                        4.583  0.529   5.125
GetCounts                          4.502  0.533   5.048
* 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-arm64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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)