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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings FlowSOM_2.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.9.0’
* 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 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 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 ... NOTE
PlotManualBars: no visible binding for global variable ‘MC’
PlotManualBars: no visible binding for global variable ‘Manual’
Undefined global functions or variables:
  MC Manual
* 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
PlotDimRed                        89.702  0.192  89.849
FlowSOMmary                       81.062  0.339  81.229
UpdateMetaclusters                21.535  0.435  21.971
PlotMarker                        21.445  0.100  21.545
PlotOutliers                      21.267  0.060  21.328
PlotStars                         18.910  0.072  18.982
GroupStats                        16.742  0.076  16.821
FlowSOM                           15.937  0.128  16.066
PlotGroups                        15.128  0.044  15.172
AddAnnotation                     11.927  0.448  12.381
query_multiple                    11.436  0.096  11.532
QueryMultiple                     11.313  0.068  11.381
PlotManualBars                    10.618  0.036  10.655
Plot2DScatters                    10.417  0.028  10.412
GetFlowJoLabels                    9.566  0.100   9.693
CountGroups                        9.058  0.096   9.153
PlotVariable                       8.861  0.064   8.925
PlotNode                           8.863  0.036   8.899
QueryStarPlot                      8.686  0.016   8.702
PlotNumbers                        8.528  0.044   8.572
PlotPies                           8.515  0.028   8.543
SaveClustersToFCS                  7.663  0.236   7.899
PlotFlowSOM                        7.783  0.040   7.822
UpdateNodeSize                     7.617  0.124   7.741
TestOutliers                       7.047  0.184   7.230
GetFeatures                        7.182  0.044   7.226
PlotLabels                         7.165  0.048   7.213
NMetaclusters                      6.938  0.052   6.989
NClusters                          6.844  0.028   6.872
MetaclusterMFIs                    6.832  0.024   6.856
PlotOverview2D                     6.294  0.052   6.346
GetMetaclusterCVs                  6.332  0.008   6.340
print.FlowSOM                      6.131  0.148   6.280
MetaclusterCVs                     6.238  0.032   6.270
GetMFIs                            6.172  0.020   6.192
GetPercentages                     6.085  0.016   6.103
GetClusterPercentagesPositive      5.989  0.096   6.086
GetMetaclusterPercentagesPositive  6.052  0.032   6.084
GetMetaclusters                    6.025  0.016   6.041
GetMetaclusterMFIs                 5.993  0.016   6.008
FlowSOMSubset                      5.851  0.064   5.915
GetClusterMFIs                     5.700  0.132   5.833
GetCounts                          5.748  0.020   5.769
GetClusters                        5.665  0.040   5.705
ReadInput                          4.886  0.256   5.142
NewData                            5.014  0.008   5.022
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘FlowSOM.Rnw’ using ‘latin-9’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c som.c -o som.o
gcc -shared -L/usr/local/lib -o FlowSOM.so som.o
installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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)