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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: 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 13.6.6
* 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 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                       61.334  2.702  67.659
PlotDimRed                        54.132  2.787  58.619
PlotMarker                        18.563  1.011  19.941
UpdateMetaclusters                18.219  1.032  19.536
PlotOutliers                      18.154  0.627  19.091
PlotStars                         14.775  0.895  16.147
FlowSOM                           13.603  0.879  14.946
PlotGroups                        13.204  0.965  14.418
GroupStats                        13.274  0.728  14.601
AddAnnotation                     10.312  0.658  13.443
QueryMultiple                     10.335  0.393  10.934
query_multiple                    10.044  0.429  10.644
Plot2DScatters                     8.930  0.530   9.691
GetFlowJoLabels                    8.676  0.631   9.460
PlotManualBars                     8.332  0.560   9.034
PlotVariable                       7.791  0.615   8.527
PlotNode                           7.531  0.624   8.279
PlotPies                           7.369  0.554   8.117
PlotNumbers                        7.270  0.540   7.924
QueryStarPlot                      7.172  0.346   7.765
CountGroups                        6.864  0.568   7.657
MetaclusterMFIs                    6.538  0.761   8.225
SaveClustersToFCS                  6.388  0.730   7.248
PlotFlowSOM                        6.418  0.611   7.131
PlotOverview2D                     6.238  0.537   6.872
PlotLabels                         6.203  0.530   6.819
NClusters                          5.995  0.644   7.330
GetFeatures                        6.074  0.374   7.119
GetMetaclusterMFIs                 5.854  0.573   6.945
NMetaclusters                      5.781  0.628   7.142
MetaclusterCVs                     5.780  0.559   6.960
UpdateNodeSize                     5.983  0.234   6.316
TestOutliers                       5.629  0.553   6.502
GetMetaclusterCVs                  5.382  0.641   6.130
print.FlowSOM                      5.428  0.592   6.094
GetPercentages                     5.408  0.534   6.513
GetMFIs                            5.343  0.561   6.028
GetMetaclusters                    5.299  0.581   6.669
GetCounts                          5.328  0.450   6.209
GetMetaclusterPercentagesPositive  5.106  0.554   6.255
GetClusters                        4.993  0.550   6.195
GetClusterMFIs                     4.918  0.538   5.674
GetClusterPercentagesPositive      4.960  0.492   6.048
FlowSOMSubset                      4.777  0.342   5.301
NewData                            4.662  0.361   5.157
* 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-1500.0.40.1)’
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)