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This page was generated on 2026-04-27 11:32 -0400 (Mon, 27 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4980
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 781/2417HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.19.4  (landing page)
Sofie Van Gassen
Snapshot Date: 2026-04-26 13:40 -0400 (Sun, 26 Apr 2026)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: devel
git_last_commit: b2d43e0
git_last_commit_date: 2026-03-17 05:41:52 -0400 (Tue, 17 Mar 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
See other builds for FlowSOM in R Universe.


CHECK results for FlowSOM on nebbiolo1

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: 2.19.4
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings FlowSOM_2.19.4.tar.gz
StartedAt: 2026-04-27 00:06:18 -0400 (Mon, 27 Apr 2026)
EndedAt: 2026-04-27 00:17:36 -0400 (Mon, 27 Apr 2026)
EllapsedTime: 678.0 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings FlowSOM_2.19.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-27 04:06:18 UTC
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.19.4’
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* 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 loading without being on the library search path ... 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 ... OK
* 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
FlowSOMmary                       58.120  0.643  59.914
PlotDimRed                        45.629  0.133  45.750
PlotOutliers                      33.321  0.214  33.618
PlotMarker                        19.034  0.028  19.062
UpdateMetaclusters                16.422  0.037  16.460
PlotStars                         14.425  0.057  14.483
GroupStats                        13.050  0.050  13.079
FlowSOM                           11.712  0.041  11.754
PlotGroups                        11.274  0.043  11.342
QueryMultiple                     10.582  0.026  10.608
query_multiple                    10.080  0.011  10.091
Plot2DScatters                    10.054  0.019  10.073
Plot1DScatters                     9.321  0.059   9.361
PlotManualBars                     8.511  0.010   8.522
AddAnnotation                      8.374  0.138   8.516
QueryStarPlot                      8.188  0.021   8.210
PlotNode                           8.074  0.087   8.160
GetFlowJoLabels                    7.933  0.073   8.007
PlotNumbers                        7.364  0.011   7.376
PlotPies                           7.300  0.053   7.353
PlotVariable                       7.316  0.009   7.325
PlotOverview2D                     6.468  0.067   6.536
GetFeatures                        6.202  0.030   6.233
PlotFlowSOM                        6.114  0.061   6.175
CountGroups                        6.121  0.043   6.163
PlotLabels                         6.145  0.006   6.151
NMetaclusters                      5.958  0.076   6.035
UpdateNodeSize                     5.999  0.018   6.016
SaveClustersToFCS                  5.704  0.012   5.716
PlotMFIHeatmap                     5.653  0.007   5.660
GetMetaclusterCVs                  5.529  0.020   5.549
GetMetaclusterPercentagesPositive  5.478  0.010   5.488
GetMFIs                            5.455  0.011   5.466
TestOutliers                       5.401  0.009   5.424
GetMajorityLabels                  5.316  0.006   5.324
NClusters                          5.208  0.003   5.214
GetMetaclusterMFIs                 5.179  0.007   5.187
GetCounts                          5.135  0.014   5.150
MetaclusterMFIs                    5.087  0.011   5.100
MetaclusterCVs                     4.999  0.057   5.056
GetPercentages                     5.031  0.009   5.041
GetMetaclusters                    5.013  0.008   5.022
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.19.4’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c som.c -o som.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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
AddAnnotation8.3740.1388.516
AggregateFlowFrames0.0860.0160.102
BuildMST1.4930.0371.530
BuildSOM1.4410.0191.460
CountGroups6.1210.0436.163
FMeasure0.0010.0010.001
FlowSOM11.712 0.04111.754
FlowSOMSubset4.5210.0244.546
FlowSOMmary58.120 0.64359.914
GetChannels0.0290.0020.030
GetClusterMFIs4.7250.0464.770
GetClusterPercentagesPositive4.7600.0244.784
GetClusters4.8400.0344.875
GetCounts5.1350.0145.150
GetFeatures6.2020.0306.233
GetFlowJoLabels7.9330.0738.007
GetMFIs5.4550.0115.466
GetMajorityLabels5.3160.0065.324
GetMarkers0.0400.0030.043
GetMetaclusterCVs5.5290.0205.549
GetMetaclusterMFIs5.1790.0075.187
GetMetaclusterPercentagesPositive5.4780.0105.488
GetMetaclusters5.0130.0085.022
GetPercentages5.0310.0095.041
GroupStats13.050 0.05013.079
Initialize_KWSP0.0030.0000.004
Initialize_PCA0.0010.0000.001
MetaClustering3.0080.0163.024
MetaclusterCVs4.9990.0575.056
MetaclusterMFIs5.0870.0115.100
NClusters5.2080.0035.214
NMetaclusters5.9580.0766.035
NewData4.2550.0104.270
Plot1DScatters9.3210.0599.361
Plot2DScatters10.054 0.01910.073
PlotCenters1.1560.0021.158
PlotClusters2D1.0880.0121.100
PlotDimRed45.629 0.13345.750
PlotFileScatters1.1300.0291.160
PlotFlowSOM6.1140.0616.175
PlotGroups11.274 0.04311.342
PlotLabels6.1450.0066.151
PlotMFIHeatmap5.6530.0075.660
PlotManualBars8.5110.0108.522
PlotMarker19.034 0.02819.062
PlotNode8.0740.0878.160
PlotNumbers7.3640.0117.376
PlotOutliers33.321 0.21433.618
PlotOverview2D6.4680.0676.536
PlotPies7.3000.0537.353
PlotSD2.6460.0102.656
PlotStarLegend0.4390.0020.440
PlotStars14.425 0.05714.483
PlotVariable7.3160.0097.325
Purity0.0010.0000.001
QueryMultiple10.582 0.02610.608
QueryStarPlot8.1880.0218.210
ReadInput3.7040.0383.742
SaveClustersToFCS5.7040.0125.716
TestOutliers5.4010.0095.424
UpdateMetaclusters16.422 0.03716.460
UpdateNodeSize5.9990.0186.016
get_channels0.0270.0000.028
get_markers0.0260.0020.028
metaClustering_consensus2.7760.0252.802
print.FlowSOM4.9700.0174.988
query_multiple10.080 0.01110.091