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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings FlowSOM_2.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.11.0’
* 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 (GCC) 10.3.1’
* 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                       92.553  0.494  93.122
PlotDimRed                        80.670  0.390  81.313
PlotMarker                        33.040  0.200  33.303
UpdateMetaclusters                29.995  0.056  30.109
PlotStars                         25.327  0.088  25.464
PlotOutliers                      24.402  0.072  24.522
GroupStats                        21.843  0.514  22.427
PlotGroups                        19.760  0.223  20.024
FlowSOM                           19.504  0.135  19.689
QueryMultiple                     19.320  0.058  19.414
query_multiple                    19.029  0.032  19.098
AddAnnotation                     15.388  0.275  15.702
Plot2DScatters                    14.953  0.088  15.064
QueryStarPlot                     13.924  0.040  13.992
PlotNumbers                       12.277  0.100  12.399
UpdateNodeSize                    11.636  0.048  11.710
PlotNode                          11.460  0.052  11.537
PlotManualBars                    11.156  0.064  11.240
GetFlowJoLabels                   11.031  0.076  11.133
PlotVariable                      10.928  0.048  10.998
PlotPies                           9.990  0.052  10.060
PlotFlowSOM                        9.212  0.138   9.385
CountGroups                        8.795  0.080   8.892
PlotLabels                         8.109  0.056   8.181
SaveClustersToFCS                  7.754  0.016   7.785
GetFeatures                        7.415  0.020   7.453
NClusters                          7.204  0.076   7.296
MetaclusterMFIs                    6.984  0.123   7.131
NMetaclusters                      6.977  0.076   7.071
MetaclusterCVs                     6.873  0.140   7.028
TestOutliers                       6.819  0.044   6.875
GetMFIs                            6.665  0.071   6.753
PlotOverview2D                     6.555  0.031   6.599
GetMetaclusterCVs                  6.444  0.024   6.480
GetMetaclusterPercentagesPositive  6.300  0.060   6.380
GetMetaclusterMFIs                 6.328  0.004   6.347
print.FlowSOM                      6.269  0.055   6.336
GetPercentages                     6.262  0.049   6.348
GetMetaclusters                    6.263  0.012   6.308
GetClusterPercentagesPositive      5.987  0.072   6.070
GetClusters                        6.010  0.016   6.040
GetCounts                          5.975  0.020   6.011
GetClusterMFIs                     5.858  0.071   5.943
FlowSOMSubset                      5.682  0.036   5.733
NewData                            5.192  0.052   5.256
ReadInput                          5.116  0.036   5.163
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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)