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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_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.2.0’
* 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
* 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 R 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 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 ... OK
* 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        89.016  2.469  91.703
PlotDimRed         69.913  1.267  71.258
UpdateMetaclusters 34.732  1.699  36.479
PlotMarker         30.783  1.669  32.494
GroupStats         25.869  1.596  27.500
PlotGroups         22.296  2.296  24.659
FlowSOM            22.015  1.612  23.660
AddAnnotation      16.447  1.012  17.483
UpdateNodeSize     15.154  0.365  15.536
query_multiple     14.955  0.384  15.361
QueryMultiple      14.286  0.475  14.928
PlotNode           12.435  1.130  13.623
PlotStars          12.103  0.978  13.150
Plot2DScatters     10.869  0.896  11.796
PlotFlowSOM        10.410  1.313  11.737
QueryStarPlot      11.276  0.401  11.734
GetFlowJoLabels    10.597  0.741  11.355
PlotManualBars     10.227  0.944  11.190
PlotNumbers         9.750  1.167  10.932
PlotPies           10.040  0.783  10.835
CountGroups         8.084  0.898   8.993
PlotLabels          7.291  0.959   8.264
TestOutliers        7.073  0.975   8.064
SaveClustersToFCS   6.968  1.020   8.089
NMetaclusters       6.665  1.057   7.742
PlotVariable        6.995  0.636   7.640
MetaclusterMFIs     6.681  0.920   7.617
NClusters           6.512  0.762   7.289
GetFeatures         6.770  0.332   7.111
GetMetaclusterCVs   6.050  0.849   6.922
GetMetaclusters     5.814  1.014   6.839
FlowSOMSubset       6.384  0.427   6.827
GetPercentages      5.791  1.020   6.822
MetaclusterCVs      5.798  0.999   6.811
GetClusterMFIs      6.207  0.491   6.732
GetMetaclusterMFIs  5.839  0.810   6.660
print.FlowSOM       5.838  0.780   6.626
ReadInput           5.749  0.847   6.601
GetMFIs             5.741  0.854   6.621
PlotOverview2D      5.809  0.743   6.558
GetCounts           5.919  0.516   6.482
GetClusters         5.803  0.469   6.282
NewData             5.235  0.489   5.737
MetaClustering      4.634  0.682   5.329
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-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/4.1/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c som.c -o som.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/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)