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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_2.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/FlowSOM.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 ‘2.13.0’
* 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                       61.715  2.769  65.502
PlotDimRed                        51.515  2.824  54.898
PlotMarker                        18.766  1.068  20.082
UpdateMetaclusters                17.771  1.196  19.061
PlotOutliers                      17.396  0.654  18.150
PlotStars                         15.036  0.928  16.036
FlowSOM                           13.597  1.107  15.116
GroupStats                        13.454  0.826  14.778
PlotGroups                        11.323  0.948  12.372
AddAnnotation                     10.311  0.667  13.441
query_multiple                    10.239  0.500  10.776
QueryMultiple                     10.136  0.504  10.710
Plot2DScatters                     8.883  0.684   9.766
GetFlowJoLabels                    8.691  0.601   9.452
PlotManualBars                     7.883  0.603   8.546
PlotPies                           7.683  0.768   8.597
PlotNode                           7.601  0.682   8.324
QueryStarPlot                      7.762  0.415   8.209
PlotVariable                       7.309  0.687   8.091
CountGroups                        7.309  0.573   8.872
PlotNumbers                        6.949  0.679   7.680
PlotFlowSOM                        6.848  0.665   7.561
SaveClustersToFCS                  6.737  0.719   7.512
NClusters                          6.012  0.635   6.764
NMetaclusters                      6.020  0.619   6.805
MetaclusterMFIs                    5.900  0.680   6.608
PlotLabels                         6.009  0.535   6.577
UpdateNodeSize                     6.264  0.242   6.553
MetaclusterCVs                     5.784  0.649   6.478
TestOutliers                       5.705  0.709   6.447
GetFeatures                        5.970  0.345   6.451
GetMetaclusterPercentagesPositive  5.658  0.644   6.330
GetPercentages                     5.368  0.746   6.465
GetMetaclusters                    5.348  0.704   6.160
print.FlowSOM                      5.330  0.699   6.060
PlotOverview2D                     5.459  0.567   6.060
GetMetaclusterMFIs                 5.288  0.664   6.005
GetMetaclusterCVs                  5.271  0.635   5.937
GetMFIs                            5.242  0.532   5.800
GetCounts                          5.020  0.586   5.687
GetClusters                        4.976  0.555   5.602
GetClusterMFIs                     4.928  0.586   5.546
GetClusterPercentagesPositive      4.864  0.487   5.390
NewData                            4.599  0.383   5.055
* 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-mac-arm64/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)