##############################################################################
##############################################################################
###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 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        48.038  0.512  48.318
PlotDimRed         44.435  0.214  44.592
PlotOutliers       17.508  0.069  17.577
PlotMarker         15.740  0.043  15.783
UpdateMetaclusters 15.615  0.087  15.702
PlotStars          13.186  0.081  13.268
GroupStats         12.299  0.041  12.341
FlowSOM            10.741  0.105  10.846
PlotGroups         10.331  0.025  10.356
AddAnnotation       8.379  0.239   8.619
QueryMultiple       8.546  0.035   8.581
Plot2DScatters      8.414  0.015   8.417
query_multiple      8.226  0.008   8.234
PlotManualBars      7.424  0.004   7.428
QueryStarPlot       7.336  0.015   7.351
GetFlowJoLabels     6.871  0.073   6.946
PlotNode            6.794  0.031   6.826
PlotPies            6.442  0.012   6.453
PlotVariable        6.309  0.006   6.315
PlotNumbers         6.279  0.015   6.295
CountGroups         5.588  0.097   5.686
PlotFlowSOM         5.589  0.063   5.652
SaveClustersToFCS   5.568  0.027   5.596
GetPercentages      5.568  0.018   5.586
UpdateNodeSize      5.359  0.009   5.369
MetaclusterMFIs     5.278  0.010   5.288
PlotLabels          5.206  0.011   5.217
NClusters           5.126  0.014   5.142
NMetaclusters       5.108  0.011   5.119
GetFeatures         5.043  0.008   5.051
* 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.