##############################################################################
##############################################################################
###
### 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_2.7.7.tar.gz
###
##############################################################################
##############################################################################


* 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 ‘2.7.7’
* 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 ‘Freq’
PlotManualBars: no visible binding for global variable ‘MC’
PlotManualBars: no visible binding for global variable ‘Manual’
PlotManualBars: no visible binding for global variable ‘C’
Undefined global functions or variables:
  C Freq MC Manual
Consider adding
  importFrom("stats", "C")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in documentation object 'PlotOutliers'
  ‘outlier_report’
Documented arguments not in \usage in documentation object 'PlotOutliers':
  ‘outlierReport’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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                        87.809  0.132  87.947
FlowSOMmary                       77.543  0.284  77.832
UpdateMetaclusters                22.301  0.072  22.375
PlotMarker                        21.767  0.108  21.878
PlotOutliers                      21.118  0.020  21.139
PlotStars                         18.851  0.096  18.949
GroupStats                        16.783  0.044  16.828
FlowSOM                           16.226  0.144  16.371
PlotGroups                        15.219  0.100  15.319
AddAnnotation                     12.068  0.160  12.231
query_multiple                    11.154  0.060  11.215
QueryMultiple                     11.168  0.028  11.196
PlotManualBars                    10.593  0.032  10.626
Plot2DScatters                    10.266  0.040  10.274
GetFlowJoLabels                    9.790  0.060   9.855
CountGroups                        8.922  0.124   9.047
PlotNumbers                        8.897  0.068   8.966
PlotVariable                       8.827  0.036   8.863
PlotNode                           8.781  0.036   8.818
PlotPies                           8.593  0.060   8.654
QueryStarPlot                      8.633  0.020   8.654
PlotFlowSOM                        8.177  0.044   8.222
SaveClustersToFCS                  8.021  0.047   8.069
UpdateNodeSize                     7.912  0.028   7.940
PlotLabels                         7.435  0.008   7.444
NClusters                          7.201  0.024   7.226
PlotOverview2D                     7.199  0.008   7.207
GetFeatures                        7.073  0.068   7.141
NMetaclusters                      6.882  0.020   6.903
MetaclusterMFIs                    6.802  0.056   6.860
TestOutliers                       6.757  0.008   6.765
GetMFIs                            6.426  0.068   6.494
GetClusters                        6.342  0.004   6.347
print.FlowSOM                      6.284  0.024   6.308
GetMetaclusterCVs                  6.226  0.024   6.251
MetaclusterCVs                     6.172  0.019   6.192
GetPercentages                     6.128  0.016   6.144
GetMetaclusterMFIs                 6.039  0.008   6.048
GetMetaclusterPercentagesPositive  5.948  0.020   5.969
GetMetaclusters                    5.948  0.016   5.965
GetClusterMFIs                     5.761  0.072   5.837
FlowSOMSubset                      5.754  0.076   5.830
GetClusterPercentagesPositive      5.774  0.016   5.790
GetCounts                          5.740  0.012   5.753
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* 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)