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This page was generated on 2025-10-22 12:06 -0400 (Wed, 22 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4890
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4680
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4625
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 762/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.17.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2025-10-21 13:45 -0400 (Tue, 21 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    NA  


CHECK results for FlowSOM on kjohnson3

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: 2025-10-21 19:48:16 -0400 (Tue, 21 Oct 2025)
EndedAt: 2025-10-21 19:51:52 -0400 (Tue, 21 Oct 2025)
EllapsedTime: 215.7 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: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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 15.0.0 (clang-1500.1.0.2.5)’
* 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        19.127  1.119  20.279
PlotDimRed         16.727  1.616  18.471
PlotOutliers        9.650  0.321  10.022
PlotMarker          6.365  0.568   6.969
UpdateMetaclusters  5.761  0.622   6.404
PlotStars           4.994  0.537   5.565
PlotGroups          4.615  0.696   5.528
* 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-arm64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.17.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch arm64 -std=gnu2x -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 -std=gnu2x -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
installing to /Library/Frameworks/R.framework/Versions/4.5-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)

Tests output


Example timings

FlowSOM.Rcheck/FlowSOM-Ex.timings

nameusersystemelapsed
AddAnnotation2.9700.1843.191
AggregateFlowFrames0.0310.0020.033
BuildMST0.5600.0340.598
BuildSOM0.3870.0350.425
CountGroups2.2290.2302.496
FMeasure0.0010.0000.001
FlowSOM4.3630.3304.723
FlowSOMSubset1.5430.1311.697
FlowSOMmary19.127 1.11920.279
GetChannels0.0140.0010.015
GetClusterMFIs1.6230.2031.831
GetClusterPercentagesPositive1.6320.2261.860
GetClusters1.6250.2701.941
GetCounts1.8340.3102.188
GetFeatures1.9890.1692.198
GetFlowJoLabels2.8120.2813.134
GetMFIs1.7340.2692.003
GetMarkers0.0130.0010.014
GetMetaclusterCVs1.7230.2411.969
GetMetaclusterMFIs1.6810.2631.945
GetMetaclusterPercentagesPositive1.7550.2762.033
GetMetaclusters1.7060.2911.997
GetPercentages1.7070.3052.027
GroupStats4.4070.4114.850
Initialize_KWSP0.0020.0000.002
Initialize_PCA000
MetaClustering1.4390.1941.642
MetaclusterCVs1.7790.3102.109
MetaclusterMFIs1.9530.3842.356
NClusters1.9160.3892.389
NMetaclusters1.9600.4092.409
NewData1.5160.2551.782
Plot2DScatters3.3590.3223.780
PlotCenters0.4200.0440.464
PlotClusters2D0.4030.0640.466
PlotDimRed16.727 1.61618.471
PlotFileScatters0.3840.0290.413
PlotFlowSOM2.1280.3452.476
PlotGroups4.6150.6965.528
PlotLabels2.2310.3502.647
PlotManualBars2.9510.3963.389
PlotMarker6.3650.5686.969
PlotNode2.7190.3423.068
PlotNumbers2.4930.3402.846
PlotOutliers 9.650 0.32110.022
PlotOverview2D2.0230.3102.340
PlotPies2.6000.3022.905
PlotSD0.7770.0860.865
PlotStars4.9940.5375.565
PlotVariable2.5900.3662.983
Purity0.0000.0000.001
QueryMultiple3.4710.2593.791
QueryStarPlot2.8210.2143.045
ReadInput1.0580.2661.336
SaveClustersToFCS2.0820.3982.488
TestOutliers1.9150.2882.217
UpdateMetaclusters5.7610.6226.404
UpdateNodeSize1.9740.1282.117
get_channels0.0130.0020.015
get_markers0.0130.0010.014
metaClustering_consensus0.8530.0680.922
plotStarLegend0.1770.0020.179
print.FlowSOM1.7800.3382.141
query_multiple3.3760.2313.609