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This page was generated on 2025-09-30 12:03 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 757/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.17.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2025-09-29 13:45 -0400 (Mon, 29 Sep 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 12.7.1 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings FlowSOM_2.17.0.tar.gz
StartedAt: 2025-09-30 00:09:20 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 00:19:15 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 594.7 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings FlowSOM_2.17.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
FlowSOMmary        49.432  0.400  49.649
PlotDimRed         43.618  0.184  43.767
PlotOutliers       30.156  0.008  30.165
PlotMarker         17.693  0.072  17.810
UpdateMetaclusters 15.708  0.063  15.771
PlotStars          14.320  0.016  14.337
GroupStats         11.602  0.021  11.623
FlowSOM            10.553  0.030  10.584
PlotGroups         10.461  0.028  10.489
QueryMultiple       9.369  0.011   9.381
query_multiple      9.146  0.016   9.163
Plot2DScatters      9.017  0.020   9.027
AddAnnotation       8.534  0.229   8.764
PlotManualBars      7.817  0.011   7.829
PlotNode            7.375  0.026   7.416
QueryStarPlot       7.236  0.006   7.296
GetFlowJoLabels     6.919  0.086   7.006
PlotVariable        6.974  0.013   6.987
PlotPies            6.917  0.020   6.947
PlotNumbers         6.650  0.013   6.679
UpdateNodeSize      5.854  0.016   5.870
CountGroups         5.726  0.039   5.766
PlotFlowSOM         5.496  0.041   5.537
SaveClustersToFCS   5.257  0.020   5.277
MetaclusterMFIs     5.217  0.006   5.223
PlotOverview2D      5.041  0.065   5.111
GetFeatures         4.980  0.066   5.047
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.17.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-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-3.22-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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
AddAnnotation8.5340.2298.764
AggregateFlowFrames0.0770.0030.079
BuildMST1.3200.0201.339
BuildSOM1.0350.0331.068
CountGroups5.7260.0395.766
FMeasure0.0010.0000.002
FlowSOM10.553 0.03010.584
FlowSOMSubset3.8560.0123.868
FlowSOMmary49.432 0.40049.649
GetChannels0.0330.0010.034
GetClusterMFIs3.8300.0223.860
GetClusterPercentagesPositive3.9630.0123.975
GetClusters3.9350.0754.011
GetCounts4.2770.0084.285
GetFeatures4.9800.0665.047
GetFlowJoLabels6.9190.0867.006
GetMFIs4.2920.0514.343
GetMarkers0.0280.0000.029
GetMetaclusterCVs4.2570.0444.302
GetMetaclusterMFIs4.1590.0054.165
GetMetaclusterPercentagesPositive4.1630.0544.218
GetMetaclusters4.0810.0144.095
GetPercentages4.0430.0504.093
GroupStats11.602 0.02111.623
Initialize_KWSP0.0040.0000.003
Initialize_PCA0.0000.0000.001
MetaClustering2.8500.0252.876
MetaclusterCVs4.2450.0094.254
MetaclusterMFIs5.2170.0065.223
NClusters4.8240.0124.837
NMetaclusters4.6460.0164.663
NewData3.8010.0063.808
Plot2DScatters9.0170.0209.027
PlotCenters1.0620.0341.095
PlotClusters2D0.9820.0020.984
PlotDimRed43.618 0.18443.767
PlotFileScatters1.0710.0151.086
PlotFlowSOM5.4960.0415.537
PlotGroups10.461 0.02810.489
PlotLabels4.9550.0124.967
PlotManualBars7.8170.0117.829
PlotMarker17.693 0.07217.810
PlotNode7.3750.0267.416
PlotNumbers6.6500.0136.679
PlotOutliers30.156 0.00830.165
PlotOverview2D5.0410.0655.111
PlotPies6.9170.0206.947
PlotSD1.9190.0191.938
PlotStars14.320 0.01614.337
PlotVariable6.9740.0136.987
Purity0.0010.0000.001
QueryMultiple9.3690.0119.381
QueryStarPlot7.2360.0067.296
ReadInput2.7050.0352.739
SaveClustersToFCS5.2570.0205.277
TestOutliers4.6310.0104.642
UpdateMetaclusters15.708 0.06315.771
UpdateNodeSize5.8540.0165.870
get_channels0.0270.0000.027
get_markers0.0270.0000.027
metaClustering_consensus2.1860.0112.217
plotStarLegend0.4360.0020.438
print.FlowSOM4.2140.0094.234
query_multiple9.1460.0169.163