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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings FlowSOM_2.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/FlowSOM.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.6.0’
* 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
* 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 ... OK
* 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        47.784  0.403  48.190
PlotDimRed         45.449  0.064  45.514
PlotMarker         16.846  0.044  16.891
UpdateMetaclusters 15.372  0.060  15.434
PlotStars          13.387  0.048  13.435
GroupStats         12.960  0.048  13.008
PlotGroups         11.177  0.092  11.269
FlowSOM            11.005  0.128  11.146
AddAnnotation       8.014  0.220   8.235
GetFlowJoLabels     8.108  0.079   8.188
QueryMultiple       8.146  0.008   8.154
query_multiple      7.955  0.016   7.971
Plot2DScatters      7.940  0.004   7.943
PlotManualBars      7.158  0.032   7.191
PlotVariable        6.622  0.028   6.650
PlotNode            6.500  0.064   6.564
PlotPies            6.318  0.020   6.338
PlotNumbers         6.051  0.032   6.083
QueryStarPlot       6.036  0.008   6.044
CountGroups         5.865  0.091   5.958
PlotFlowSOM         5.797  0.020   5.817
UpdateNodeSize      5.485  0.028   5.512
NMetaclusters       5.468  0.036   5.504
GetFeatures         5.421  0.040   5.462
SaveClustersToFCS   5.273  0.040   5.314
PlotLabels          5.179  0.012   5.192
MetaclusterMFIs     5.067  0.028   5.095
NClusters           4.946  0.064   5.009
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL FlowSOM
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/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)