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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings FlowSOM_2.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
FlowSOMmary        47.176  0.470  47.314
PlotDimRed         42.305  0.155  42.386
PlotOutliers       16.670  0.016  16.687
PlotMarker         16.297  0.092  16.390
UpdateMetaclusters 15.350  0.040  15.390
PlotStars          13.594  0.052  13.647
GroupStats         11.523  0.067  11.590
FlowSOM            11.006  0.120  11.126
PlotGroups         10.217  0.136  10.360
query_multiple      8.998  0.016   9.014
AddAnnotation       8.415  0.156   8.573
QueryMultiple       8.506  0.048   8.554
Plot2DScatters      7.341  0.060   7.370
GetFlowJoLabels     7.025  0.088   7.113
PlotManualBars      6.947  0.036   6.984
PlotNode            6.653  0.028   6.682
QueryStarPlot       6.393  0.028   6.421
PlotVariable        6.380  0.028   6.409
PlotNumbers         6.324  0.072   6.398
PlotPies            6.113  0.020   6.132
CountGroups         5.751  0.104   5.855
UpdateNodeSize      5.801  0.048   5.850
NMetaclusters       5.430  0.012   5.442
PlotFlowSOM         5.273  0.048   5.320
MetaclusterMFIs     5.058  0.020   5.079
PlotLabels          5.002  0.020   5.023
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.