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This page was generated on 2025-10-18 12:04 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 761/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.17.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: devel
git_last_commit: d549275
git_last_commit_date: 2025-04-15 10:36:59 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for FlowSOM on lconway

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: 2.17.0
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_2.17.0.tar.gz
StartedAt: 2025-10-17 22:14:21 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 22:26:39 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 738.0 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_2.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘2.17.0’
* 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: ‘MacOSX11.3.1.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                       51.983  3.196  62.287
PlotDimRed                        44.187  3.461  51.850
PlotOutliers                      35.511  1.502  39.481
UpdateMetaclusters                18.854  1.619  21.101
PlotMarker                        17.056  1.626  23.571
PlotStars                         16.567  1.232  18.287
GroupStats                        13.646  1.351  16.371
PlotGroups                        13.544  1.227  14.987
FlowSOM                           12.444  1.562  15.438
Plot2DScatters                    10.854  1.082  12.666
PlotManualBars                     9.882  1.309  12.878
query_multiple                    10.427  0.656  12.707
QueryMultiple                     10.078  0.722  14.356
AddAnnotation                      9.606  0.917  12.237
GetFlowJoLabels                    8.076  0.978   9.445
PlotNumbers                        7.825  1.020   9.772
PlotNode                           7.335  1.135  11.131
PlotVariable                       7.226  1.189  10.700
PlotPies                           6.683  1.233  12.585
QueryStarPlot                      7.209  0.484   9.508
UpdateNodeSize                     7.264  0.326   7.708
SaveClustersToFCS                  5.588  1.338   9.175
GetFeatures                        6.135  0.695   7.556
PlotFlowSOM                        5.891  0.874   6.862
PlotLabels                         5.887  0.876   7.752
NMetaclusters                      5.555  1.073   8.258
CountGroups                        5.762  0.821   8.252
PlotOverview2D                     5.316  0.929   7.001
TestOutliers                       4.944  1.234   7.387
MetaclusterMFIs                    4.769  1.303  10.249
NClusters                          4.910  1.161   9.994
GetMFIs                            4.708  1.252   9.092
GetMetaclusterCVs                  4.564  1.195   6.671
GetMetaclusters                    4.808  0.933   6.029
GetMetaclusterMFIs                 4.765  0.865   5.732
GetPercentages                     4.790  0.825   5.768
GetMetaclusterPercentagesPositive  4.703  0.871   5.717
print.FlowSOM                      4.507  1.033   5.673
MetaclusterCVs                     4.218  1.091   7.191
GetCounts                          4.527  0.754   5.535
GetClusters                        4.213  0.801   5.474
GetClusterMFIs                     4.237  0.761   7.405
FlowSOMSubset                      4.011  0.806   7.940
MetaClustering                     3.669  0.947   5.564
GetClusterPercentagesPositive      3.695  0.825   7.403
NewData                            3.769  0.688   5.406
ReadInput                          3.021  1.148   8.840
* 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-3.22-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 ‘2.17.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.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
AddAnnotation 9.606 0.91712.237
AggregateFlowFrames0.1100.0220.163
BuildMST1.5700.1121.730
BuildSOM1.2620.1121.409
CountGroups5.7620.8218.252
FMeasure0.0010.0000.002
FlowSOM12.444 1.56215.438
FlowSOMSubset4.0110.8067.940
FlowSOMmary51.983 3.19662.287
GetChannels0.0430.0060.050
GetClusterMFIs4.2370.7617.405
GetClusterPercentagesPositive3.6950.8257.403
GetClusters4.2130.8015.474
GetCounts4.5270.7545.535
GetFeatures6.1350.6957.556
GetFlowJoLabels8.0760.9789.445
GetMFIs4.7081.2529.092
GetMarkers0.0450.0050.053
GetMetaclusterCVs4.5641.1956.671
GetMetaclusterMFIs4.7650.8655.732
GetMetaclusterPercentagesPositive4.7030.8715.717
GetMetaclusters4.8080.9336.029
GetPercentages4.7900.8255.768
GroupStats13.646 1.35116.371
Initialize_KWSP0.0060.0010.006
Initialize_PCA0.0010.0010.001
MetaClustering3.6690.9475.564
MetaclusterCVs4.2181.0917.191
MetaclusterMFIs 4.769 1.30310.249
NClusters4.9101.1619.994
NMetaclusters5.5551.0738.258
NewData3.7690.6885.406
Plot2DScatters10.854 1.08212.666
PlotCenters1.5180.1521.794
PlotClusters2D1.4240.1601.629
PlotDimRed44.187 3.46151.850
PlotFileScatters1.4620.0681.569
PlotFlowSOM5.8910.8746.862
PlotGroups13.544 1.22714.987
PlotLabels5.8870.8767.752
PlotManualBars 9.882 1.30912.878
PlotMarker17.056 1.62623.571
PlotNode 7.335 1.13511.131
PlotNumbers7.8251.0209.772
PlotOutliers35.511 1.50239.481
PlotOverview2D5.3160.9297.001
PlotPies 6.683 1.23312.585
PlotSD2.2010.3663.254
PlotStars16.567 1.23218.287
PlotVariable 7.226 1.18910.700
Purity0.0010.0000.001
QueryMultiple10.078 0.72214.356
QueryStarPlot7.2090.4849.508
ReadInput3.0211.1488.840
SaveClustersToFCS5.5881.3389.175
TestOutliers4.9441.2347.387
UpdateMetaclusters18.854 1.61921.101
UpdateNodeSize7.2640.3267.708
get_channels0.0390.0030.042
get_markers0.0400.0040.045
metaClustering_consensus2.4910.5263.085
plotStarLegend0.4820.0050.493
print.FlowSOM4.5071.0335.673
query_multiple10.427 0.65612.707