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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: x86_64-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 Monterey 12.7.1
* 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 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                       53.014  2.528  55.811
PlotDimRed                        42.999  2.653  46.343
PlotMarker                        20.555  1.410  22.309
PlotOutliers                      20.060  1.080  21.479
UpdateMetaclusters                17.327  1.424  19.140
PlotStars                         16.071  1.158  17.482
GroupStats                        14.792  0.961  15.930
PlotGroups                        12.810  1.249  14.310
FlowSOM                           12.780  1.162  14.126
AddAnnotation                     10.342  0.738  11.213
QueryMultiple                     10.276  0.559  11.019
query_multiple                    10.260  0.559  10.980
Plot2DScatters                     8.618  0.797   9.553
PlotManualBars                     8.281  0.886   9.320
GetFlowJoLabels                    8.329  0.801   9.268
QueryStarPlot                      7.883  0.380   8.404
PlotNode                           7.464  0.774   8.386
PlotVariable                       7.220  0.912   8.273
PlotNumbers                        7.078  0.883   8.114
PlotPies                           6.991  0.870   8.008
CountGroups                        6.449  0.636   7.188
UpdateNodeSize                     6.745  0.322   7.174
SaveClustersToFCS                  5.707  1.052   6.903
MetaclusterMFIs                    5.927  0.810   6.843
NClusters                          5.694  0.999   6.787
PlotFlowSOM                        5.940  0.734   6.764
TestOutliers                       5.661  1.008   6.876
PlotLabels                         5.811  0.711   6.628
NMetaclusters                      5.625  0.842   6.580
GetFeatures                        5.883  0.466   6.421
MetaclusterCVs                     5.191  0.780   6.077
PlotOverview2D                     5.181  0.773   6.068
GetMFIs                            4.941  0.798   5.805
GetMetaclusterMFIs                 4.835  0.732   5.648
GetMetaclusters                    4.776  0.762   5.661
GetMetaclusterCVs                  4.692  0.821   5.575
print.FlowSOM                      4.726  0.677   5.487
GetPercentages                     4.699  0.689   5.462
GetMetaclusterPercentagesPositive  4.612  0.731   5.422
NewData                            4.561  0.572   5.229
FlowSOMSubset                      4.600  0.470   5.171
GetClusterMFIs                     4.365  0.597   5.034
* 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-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** 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/4.4-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)