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This page was generated on 2025-10-09 11:38 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 756/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.16.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2025-10-06 13:40 -0400 (Mon, 06 Oct 2025)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: RELEASE_3_21
git_last_commit: 4bdaa3d
git_last_commit_date: 2025-04-15 10:36:59 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for FlowSOM on merida1

To the developers/maintainers of the FlowSOM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FlowSOM.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: FlowSOM
Version: 2.16.0
Command: /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_2.16.0.tar.gz
StartedAt: 2025-10-07 03:50:12 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 04:09:09 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 1136.9 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /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_2.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.16.0’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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                       98.120  2.515 104.317
PlotDimRed                        73.942  2.984  78.865
PlotOutliers                      69.289  1.253  73.771
PlotMarker                        37.051  1.508  39.874
UpdateMetaclusters                34.052  1.489  36.195
PlotStars                         29.579  1.016  31.913
GroupStats                        27.922  1.133  30.717
PlotGroups                        23.522  1.413  26.202
FlowSOM                           23.261  1.517  25.162
Plot2DScatters                    21.992  1.078  24.314
QueryMultiple                     20.970  0.615  23.519
query_multiple                    20.302  0.600  21.319
AddAnnotation                     17.896  0.733  19.108
PlotManualBars                    17.196  1.127  18.681
QueryStarPlot                     14.864  0.447  16.001
PlotNode                          13.863  1.032  15.375
GetFlowJoLabels                   14.063  0.799  15.300
UpdateNodeSize                    13.953  0.486  14.761
PlotPies                          13.150  1.007  15.562
PlotNumbers                       13.000  0.952  14.288
PlotVariable                      12.681  0.934  14.363
GetFeatures                       12.201  0.406  13.345
CountGroups                       11.469  0.687  12.558
PlotFlowSOM                       10.802  0.955  11.930
SaveClustersToFCS                  9.582  1.121  10.769
PlotLabels                         9.850  0.797  11.423
NMetaclusters                      9.190  1.398  10.805
NClusters                          9.273  1.030  10.849
MetaclusterMFIs                    9.157  0.971  10.319
PlotOverview2D                     8.651  0.878  10.276
TestOutliers                       8.564  0.746   9.370
GetMetaclusterCVs                  8.322  0.985   9.429
MetaclusterCVs                     8.137  1.011   9.358
GetMFIs                            8.061  0.924   9.261
GetMetaclusterMFIs                 8.029  0.948   9.139
FlowSOMSubset                      8.405  0.565   9.526
GetPercentages                     8.073  0.889   9.059
print.FlowSOM                      7.940  1.007   9.142
GetMetaclusters                    7.859  0.906   9.031
GetMetaclusterPercentagesPositive  7.810  0.938   8.946
GetClusterMFIs                     7.736  0.813   8.800
GetCounts                          7.830  0.674   8.750
NewData                            7.558  0.809   8.478
GetClusterPercentagesPositive      7.682  0.671   8.498
GetClusters                        7.529  0.639   8.289
MetaClustering                     6.422  0.809   7.668
ReadInput                          6.370  0.668   7.311
metaClustering_consensus           4.967  0.478   5.568
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.16.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/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)

Tests output


Example timings

FlowSOM.Rcheck/FlowSOM-Ex.timings

nameusersystemelapsed
AddAnnotation17.896 0.73319.108
AggregateFlowFrames0.1730.0080.184
BuildMST2.7530.1002.892
BuildSOM2.5410.1362.775
CountGroups11.469 0.68712.558
FMeasure0.0030.0000.004
FlowSOM23.261 1.51725.162
FlowSOMSubset8.4050.5659.526
FlowSOMmary 98.120 2.515104.317
GetChannels0.0690.0050.075
GetClusterMFIs7.7360.8138.800
GetClusterPercentagesPositive7.6820.6718.498
GetClusters7.5290.6398.289
GetCounts7.8300.6748.750
GetFeatures12.201 0.40613.345
GetFlowJoLabels14.063 0.79915.300
GetMFIs8.0610.9249.261
GetMarkers0.0710.0040.076
GetMetaclusterCVs8.3220.9859.429
GetMetaclusterMFIs8.0290.9489.139
GetMetaclusterPercentagesPositive7.8100.9388.946
GetMetaclusters7.8590.9069.031
GetPercentages8.0730.8899.059
GroupStats27.922 1.13330.717
Initialize_KWSP0.0130.0000.016
Initialize_PCA0.0010.0010.003
MetaClustering6.4220.8097.668
MetaclusterCVs8.1371.0119.358
MetaclusterMFIs 9.157 0.97110.319
NClusters 9.273 1.03010.849
NMetaclusters 9.190 1.39810.805
NewData7.5580.8098.478
Plot2DScatters21.992 1.07824.314
PlotCenters2.5590.1202.876
PlotClusters2D2.3300.1622.524
PlotDimRed73.942 2.98478.865
PlotFileScatters2.8160.0532.911
PlotFlowSOM10.802 0.95511.930
PlotGroups23.522 1.41326.202
PlotLabels 9.850 0.79711.423
PlotManualBars17.196 1.12718.681
PlotMarker37.051 1.50839.874
PlotNode13.863 1.03215.375
PlotNumbers13.000 0.95214.288
PlotOutliers69.289 1.25373.771
PlotOverview2D 8.651 0.87810.276
PlotPies13.150 1.00715.562
PlotSD4.3590.1694.687
PlotStars29.579 1.01631.913
PlotVariable12.681 0.93414.363
Purity0.0020.0010.003
QueryMultiple20.970 0.61523.519
QueryStarPlot14.864 0.44716.001
ReadInput6.3700.6687.311
SaveClustersToFCS 9.582 1.12110.769
TestOutliers8.5640.7469.370
UpdateMetaclusters34.052 1.48936.195
UpdateNodeSize13.953 0.48614.761
get_channels0.0630.0030.067
get_markers0.0640.0040.069
metaClustering_consensus4.9670.4785.568
plotStarLegend1.0240.0111.098
print.FlowSOM7.9401.0079.142
query_multiple20.302 0.60021.319