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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings FlowSOM_2.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/FlowSOM.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.4.0’
* 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 ... NOTE
Plot2DScatters: no visible binding for global variable ‘Population’
Undefined global functions or variables:
  Population
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
FlowSOMmary                   47.047  0.240  47.287
PlotDimRed                    44.081  0.048  44.129
PlotMarker                    16.311  0.060  16.371
UpdateMetaclusters            15.557  0.068  15.627
GroupStats                    12.084  0.048  12.132
FlowSOM                       11.597  0.133  11.729
PlotGroups                    11.617  0.024  11.642
QueryMultiple                  7.980  0.024   8.003
AddAnnotation                  7.587  0.239   7.829
query_multiple                 7.445  0.020   7.465
Plot2DScatters                 7.145  0.012   7.156
PlotFlowSOM                    7.076  0.076   7.152
PlotManualBars                 7.071  0.016   7.087
GetFlowJoLabels                6.831  0.016   6.848
PlotNumbers                    6.559  0.016   6.576
PlotPies                       6.323  0.032   6.354
PlotNode                       6.338  0.008   6.346
QueryStarPlot                  6.231  0.012   6.242
PlotStars                      6.173  0.028   6.201
CountGroups                    5.962  0.064   6.026
GetFeatures                    5.672  0.008   5.680
PlotVariable                   5.536  0.004   5.540
SaveClustersToFCS              5.053  0.040   5.093
GetClusterPercentagesPositive  5.013  0.044   5.057
UpdateNodeSize                 5.031  0.024   5.055
PlotLabels                     5.017  0.020   5.037
GetMetaclusterCVs              4.953  0.052   5.005
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL FlowSOM
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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)