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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FlowSOM_2.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.14.0’
* 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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        49.150  0.412  49.333
PlotDimRed         44.341  0.119  44.415
PlotOutliers       17.407  0.082  17.489
PlotMarker         15.766  0.035  15.802
UpdateMetaclusters 14.939  0.082  15.022
PlotStars          13.013  0.043  13.057
GroupStats         12.003  0.111  12.115
FlowSOM            10.964  0.131  11.096
PlotGroups         10.465  0.013  10.478
QueryMultiple       8.548  0.008   8.557
AddAnnotation       8.194  0.214   8.438
Plot2DScatters      7.940  0.010   7.940
query_multiple      7.918  0.013   7.932
GetFlowJoLabels     7.045  0.132   7.178
PlotManualBars      6.968  0.006   6.975
QueryStarPlot       6.363  0.062   6.426
PlotNode            6.314  0.014   6.328
PlotPies            6.251  0.008   6.260
PlotVariable        6.122  0.010   6.132
PlotNumbers         5.970  0.007   5.976
CountGroups         5.547  0.079   5.625
UpdateNodeSize      5.401  0.024   5.425
PlotFlowSOM         5.389  0.011   5.400
PlotLabels          5.235  0.014   5.250
NClusters           5.220  0.010   5.230
GetFeatures         5.048  0.033   5.081
NMetaclusters       5.040  0.013   5.052
PlotOverview2D      4.970  0.071   5.042
* 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-3.20-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.