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### Running command:
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###   /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_2.7.10.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.7.10’
* 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* 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 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 loading without being on the library search path ... 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
FlowSOMmary        49.212  0.376  49.589
PlotDimRed         46.983  0.048  47.033
PlotMarker         18.489  0.041  18.531
UpdateMetaclusters 16.980  0.076  17.056
PlotOutliers       16.277  0.080  16.358
PlotStars          14.098  0.044  14.143
GroupStats         13.344  0.131  13.477
PlotGroups         11.934  0.056  11.990
FlowSOM            11.619  0.136  11.755
query_multiple      8.930  0.000   8.931
AddAnnotation       8.457  0.196   8.654
QueryMultiple       8.613  0.012   8.624
PlotManualBars      8.495  0.050   8.545
GetFlowJoLabels     7.667  0.117   7.783
Plot2DScatters      7.713  0.068   7.781
PlotNode            7.136  0.004   7.140
PlotNumbers         6.835  0.008   6.843
PlotVariable        6.707  0.032   6.742
PlotFlowSOM         6.632  0.100   6.732
QueryStarPlot       6.590  0.052   6.642
PlotPies            6.484  0.076   6.560
MetaclusterMFIs     5.880  0.064   5.944
NClusters           5.841  0.064   5.906
GetFeatures         5.883  0.015   5.911
CountGroups         5.767  0.124   5.891
TestOutliers        5.746  0.008   5.754
NMetaclusters       5.597  0.020   5.618
PlotLabels          5.469  0.004   5.472
MetaclusterCVs      5.277  0.048   5.328
GetMFIs             5.245  0.019   5.264
UpdateNodeSize      5.225  0.008   5.233
GetMetaclusterMFIs  5.129  0.008   5.137
PlotOverview2D      5.086  0.008   5.095
GetPercentages      5.043  0.040   5.083
SaveClustersToFCS   5.062  0.016   5.078
* 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.