##############################################################################
##############################################################################
###
### 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                       58.201  2.673  62.411
PlotDimRed                        52.338  3.514  56.715
PlotOutliers                      17.781  0.881  18.803
PlotMarker                        17.619  0.989  18.787
UpdateMetaclusters                17.133  1.145  18.383
PlotStars                         14.506  0.808  15.423
FlowSOM                           13.208  1.077  14.570
GroupStats                        12.620  0.891  13.834
PlotGroups                        11.070  1.202  12.478
AddAnnotation                      9.532  0.672  10.986
QueryMultiple                      9.410  0.508  10.051
query_multiple                     8.852  0.468   9.453
Plot2DScatters                     8.075  0.633   8.865
GetFlowJoLabels                    7.993  0.594   8.689
PlotManualBars                     7.528  0.615   8.206
PlotPies                           7.063  0.678   7.800
CountGroups                        6.975  0.553   7.775
QueryStarPlot                      7.148  0.343   7.524
PlotVariable                       6.796  0.615   7.542
PlotNode                           6.812  0.572   7.483
PlotNumbers                        6.587  0.667   7.398
SaveClustersToFCS                  6.389  0.687   7.123
NMetaclusters                      5.675  0.972   6.797
PlotLabels                         6.005  0.621   6.697
GetFeatures                        5.908  0.434   6.397
PlotFlowSOM                        5.721  0.561   6.322
MetaclusterMFIs                    5.578  0.648   6.302
NClusters                          5.586  0.622   6.292
TestOutliers                       5.471  0.640   6.147
print.FlowSOM                      5.058  0.864   5.946
UpdateNodeSize                     5.705  0.211   5.931
GetMetaclusterMFIs                 5.023  0.858   6.046
PlotOverview2D                     5.271  0.583   5.885
GetMFIs                            5.051  0.566   5.688
MetaclusterCVs                     5.043  0.538   5.666
GetPercentages                     4.962  0.549   5.576
GetMetaclusters                    4.867  0.528   5.462
GetMetaclusterCVs                  4.754  0.580   5.474
GetMetaclusterPercentagesPositive  4.763  0.548   5.415
NewData                            4.575  0.706   5.434
GetCounts                          4.622  0.573   5.257
GetClusters                        4.707  0.483   5.214
GetClusterMFIs                     4.698  0.443   5.271
GetClusterPercentagesPositive      4.684  0.441   5.273
* 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)