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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_2.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.15.0’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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                       49.471  2.369  51.992
PlotDimRed                        42.530  2.822  46.033
PlotOutliers                      20.268  0.991  21.541
PlotMarker                        18.750  1.376  20.402
UpdateMetaclusters                17.093  1.406  18.796
PlotStars                         15.103  1.236  16.621
GroupStats                        13.308  0.935  14.359
FlowSOM                           11.992  1.013  13.160
PlotGroups                        11.694  1.201  13.056
QueryMultiple                      9.543  0.550  10.235
AddAnnotation                      9.079  0.610   9.783
query_multiple                     9.232  0.425   9.764
Plot2DScatters                     8.098  0.792   8.992
PlotManualBars                     7.677  0.925   8.698
GetFlowJoLabels                    7.671  0.773   8.568
PlotNode                           7.538  0.826   8.492
PlotNumbers                        7.033  1.052   8.269
PlotPies                           6.686  0.922   7.758
PlotVariable                       6.741  0.746   7.583
QueryStarPlot                      6.998  0.355   7.448
CountGroups                        6.301  0.641   7.026
SaveClustersToFCS                  5.861  0.921   6.926
MetaclusterMFIs                    5.831  0.856   6.825
NMetaclusters                      5.697  0.819   6.632
PlotFlowSOM                        5.706  0.697   6.478
PlotLabels                         5.457  0.901   6.433
UpdateNodeSize                     6.067  0.281   6.415
GetFeatures                        5.668  0.455   6.201
NClusters                          5.406  0.686   6.164
TestOutliers                       5.251  0.798   6.175
MetaclusterCVs                     5.139  0.663   5.886
PlotOverview2D                     4.843  0.688   5.611
FlowSOMSubset                      5.006  0.419   5.487
GetMetaclusterCVs                  4.635  0.753   5.474
GetMetaclusterPercentagesPositive  4.585  0.788   5.440
print.FlowSOM                      4.645  0.696   5.399
GetPercentages                     4.604  0.734   5.417
GetMFIs                            4.574  0.680   5.346
GetMetaclusters                    4.454  0.612   5.115
GetMetaclusterMFIs                 4.297  0.655   5.009
* 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-3.21-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/4.5-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.15.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/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)