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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 4.4.0 (2024-04-24)
* 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 13.6.5
* 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 15.0.0 (clang-1500.1.0.2.5)’
* 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                       53.076  1.730  71.373
PlotDimRed                        39.223  1.669  57.191
PlotOutliers                      20.101  0.601  27.959
PlotMarker                        19.160  1.022  25.855
UpdateMetaclusters                18.414  0.892  26.084
PlotStars                         15.693  0.762  20.988
GroupStats                        14.520  0.766  20.552
FlowSOM                           14.101  0.760  19.301
PlotGroups                        12.539  0.810  17.715
AddAnnotation                     10.757  0.488  14.699
QueryMultiple                     10.720  0.427  15.190
query_multiple                    10.567  0.404  14.598
Plot2DScatters                     9.304  0.582  15.963
PlotManualBars                     8.697  0.595  12.436
GetFlowJoLabels                    8.520  0.487  12.105
PlotNumbers                        8.291  0.684  10.783
QueryStarPlot                      8.440  0.332  12.787
PlotNode                           7.967  0.654  10.686
PlotVariable                       7.762  0.544  10.640
PlotPies                           7.570  0.526  11.361
CountGroups                        7.319  0.437  10.427
PlotFlowSOM                        6.741  0.615   9.322
PlotOverview2D                     6.813  0.459  10.267
PlotLabels                         6.613  0.524  10.248
SaveClustersToFCS                  6.539  0.512   9.754
UpdateNodeSize                     6.573  0.162   9.534
GetFeatures                        6.416  0.300   9.406
NMetaclusters                      6.101  0.589   7.623
print.FlowSOM                      6.078  0.588   8.889
NClusters                          6.081  0.578   8.630
MetaclusterMFIs                    5.955  0.615   8.345
TestOutliers                       6.074  0.472   8.448
GetCounts                          6.036  0.357   8.932
GetMetaclusterPercentagesPositive  5.663  0.566   8.867
FlowSOMSubset                      5.936  0.272   8.190
GetMetaclusters                    5.563  0.559   8.658
MetaclusterCVs                     5.620  0.466   7.871
GetPercentages                     5.598  0.486   8.676
GetMetaclusterMFIs                 5.548  0.498   7.859
GetMFIs                            5.510  0.490   7.870
GetMetaclusterCVs                  5.344  0.491   7.165
GetClusterMFIs                     5.173  0.360   8.313
GetClusterPercentagesPositive      5.159  0.345   8.109
GetClusters                        5.130  0.363   8.256
NewData                            5.019  0.375   7.021
ReadInput                          4.029  0.407   6.050
* 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-arm64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
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)