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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_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.14.0’
* 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                       56.897  2.667  59.890
PlotDimRed                        51.171  3.412  55.136
PlotMarker                        16.824  1.328  18.255
UpdateMetaclusters                16.582  1.164  17.776
PlotOutliers                      16.149  0.853  17.037
PlotStars                         13.411  1.193  14.639
GroupStats                        13.408  0.974  14.452
FlowSOM                           13.066  1.088  14.294
PlotGroups                        10.664  1.475  12.266
AddAnnotation                      9.301  0.625   9.970
QueryMultiple                      9.086  0.566   9.790
query_multiple                     8.986  0.553   9.562
Plot2DScatters                     8.530  0.681   9.252
GetFlowJoLabels                    7.856  0.652   8.538
PlotManualBars                     7.675  0.761   8.464
PlotVariable                       7.629  0.802   8.480
CountGroups                        7.248  0.610   8.006
PlotNode                           6.828  0.633   7.474
QueryStarPlot                      6.753  0.436   7.190
PlotPies                           6.297  0.806   7.127
PlotNumbers                        6.288  0.743   7.053
PlotFlowSOM                        5.910  0.661   6.592
SaveClustersToFCS                  5.766  0.631   6.409
GetMFIs                            5.389  0.735   6.193
NClusters                          4.961  1.067   6.199
PlotLabels                         5.379  0.603   6.004
MetaclusterMFIs                    5.247  0.614   5.982
TestOutliers                       5.335  0.518   5.858
GetFeatures                        5.461  0.372   5.850
UpdateNodeSize                     5.412  0.230   5.650
PlotOverview2D                     5.026  0.571   5.605
print.FlowSOM                      4.903  0.680   5.643
MetaclusterCVs                     4.944  0.613   5.638
GetMetaclusters                    4.835  0.709   5.581
GetClusterPercentagesPositive      4.869  0.643   5.550
GetMetaclusterPercentagesPositive  4.807  0.645   5.514
GetMetaclusterMFIs                 4.825  0.624   5.467
GetPercentages                     4.827  0.607   5.443
GetClusters                        4.547  0.632   5.206
GetCounts                          4.492  0.593   5.097
GetClusterMFIs                     4.441  0.562   5.012
NMetaclusters                      4.344  0.655   5.390
GetMetaclusterCVs                  4.393  0.585   5.057
* 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)