##############################################################################
##############################################################################
###
### 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_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.16.0’
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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                       62.252  3.216  66.252
PlotDimRed                        52.095  4.098  56.952
PlotOutliers                      29.531  0.774  30.431
PlotMarker                        19.321  1.618  21.245
UpdateMetaclusters                17.614  1.416  19.163
PlotStars                         15.297  0.976  16.318
GroupStats                        12.996  1.359  14.663
FlowSOM                           12.832  1.014  14.011
PlotGroups                        11.680  1.457  13.290
QueryMultiple                     10.980  0.685  11.788
query_multiple                    10.701  0.623  11.343
Plot2DScatters                    10.620  0.645  11.386
AddAnnotation                      9.747  0.727  10.665
PlotManualBars                     9.221  0.992  10.368
GetFlowJoLabels                    8.686  0.752   9.482
PlotPies                           8.529  0.695   9.266
PlotNode                           7.800  1.017   8.929
PlotVariable                       7.765  0.879   8.662
QueryStarPlot                      8.126  0.446   8.590
PlotNumbers                        6.900  0.705   7.646
PlotFlowSOM                        6.394  1.183   7.711
CountGroups                        6.863  0.623   7.539
PlotOverview2D                     6.857  0.598   7.469
NClusters                          5.749  1.168   7.033
PlotLabels                         6.102  0.677   6.833
SaveClustersToFCS                  6.044  0.691   6.748
NMetaclusters                      5.454  1.244   6.779
GetMetaclusterMFIs                 5.660  0.957   6.686
GetFeatures                        5.942  0.655   6.674
print.FlowSOM                      5.752  0.773   6.550
UpdateNodeSize                     6.143  0.300   6.468
TestOutliers                       5.587  0.782   6.411
MetaclusterMFIs                    5.690  0.670   6.407
GetMetaclusterCVs                  5.199  0.989   6.244
GetClusterMFIs                     5.400  0.491   6.154
MetaclusterCVs                     5.284  0.572   5.901
GetClusters                        5.278  0.568   5.868
GetCounts                          4.998  0.831   5.904
GetMetaclusters                    5.192  0.624   5.855
GetPercentages                     5.172  0.625   5.846
GetMFIs                            5.155  0.619   5.811
GetMetaclusterPercentagesPositive  5.029  0.580   5.646
NewData                            5.037  0.464   5.555
GetClusterPercentagesPositive      4.923  0.550   5.509
FlowSOMSubset                      4.746  0.660   5.553
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.16.0’
** 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 -std=gnu2x -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 -std=gnu2x -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
installing to /Library/Frameworks/R.framework/Versions/4.5-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)