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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.13.0’
* 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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
FlowSOMmary                       60.585  2.774  64.418
PlotDimRed                        53.194  2.958  56.934
PlotMarker                        18.941  1.161  20.192
UpdateMetaclusters                17.818  1.297  19.228
PlotOutliers                      17.166  0.683  18.011
PlotStars                         15.267  1.030  16.405
GroupStats                        13.950  0.986  15.396
FlowSOM                           13.788  1.004  16.321
PlotGroups                        11.527  0.993  12.626
AddAnnotation                     10.317  0.656  12.119
query_multiple                    10.213  0.517  10.803
QueryMultiple                      9.748  0.373  10.246
Plot2DScatters                     8.958  0.653   9.905
GetFlowJoLabels                    8.725  0.700   9.629
PlotVariable                       7.709  0.730   8.484
PlotManualBars                     7.656  0.690   8.416
QueryStarPlot                      7.548  0.400   7.978
CountGroups                        7.225  0.649   9.636
PlotNode                           7.115  0.643   7.824
PlotPies                           6.847  0.758   7.641
PlotNumbers                        6.709  0.687   7.470
PlotFlowSOM                        6.327  0.613   6.981
TestOutliers                       6.240  0.680   6.953
SaveClustersToFCS                  6.197  0.696   6.923
MetaclusterMFIs                    5.834  0.729   6.615
NClusters                          5.837  0.722   6.599
GetPercentages                     5.720  0.741   6.531
NMetaclusters                      5.836  0.605   6.485
UpdateNodeSize                     6.149  0.244   6.417
PlotLabels                         5.875  0.501   6.452
GetFeatures                        5.944  0.381   6.452
print.FlowSOM                      5.300  0.757   6.096
MetaclusterCVs                     5.377  0.642   6.166
PlotOverview2D                     5.290  0.673   5.992
GetMetaclusterCVs                  5.308  0.603   6.098
GetMetaclusters                    5.192  0.651   5.883
GetMFIs                            5.238  0.576   6.107
GetMetaclusterMFIs                 5.202  0.610   5.846
GetClusters                        5.191  0.513   5.733
FlowSOMSubset                      5.270  0.369   5.681
GetClusterPercentagesPositive      4.879  0.477   5.402
GetMetaclusterPercentagesPositive  4.791  0.545   5.483
GetClusterMFIs                     4.838  0.463   5.329
GetCounts                          4.772  0.491   5.304
NewData                            4.606  0.458   5.155
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)