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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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: 2025-10-13 13:40 -0400 (Mon, 13 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 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: FlowSOM
Version: 2.16.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FlowSOM_2.16.0.tar.gz
StartedAt: 2025-10-14 09:14:08 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 09:26:56 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 768.5 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FlowSOM_2.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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                       83.389  0.318  83.781
PlotDimRed                        80.798  0.143  81.103
PlotOutliers                      43.899  0.091  44.094
PlotMarker                        25.111  0.088  25.274
UpdateMetaclusters                23.889  0.143  24.094
PlotStars                         20.539  0.032  20.613
GroupStats                        18.046  0.039  18.140
PlotGroups                        17.013  0.016  17.074
FlowSOM                           16.819  0.111  16.999
query_multiple                    14.025  0.032  14.091
Plot2DScatters                    13.873  0.052  13.983
QueryMultiple                     13.678  0.028  13.738
PlotManualBars                    12.594  0.020  12.651
AddAnnotation                     12.304  0.170  12.515
PlotNode                          10.271  0.036  10.329
QueryStarPlot                     10.046  0.020  10.084
PlotPies                          10.012  0.028  10.060
GetFlowJoLabels                    9.841  0.072   9.942
PlotNumbers                        9.627  0.016   9.665
PlotVariable                       9.438  0.028   9.491
CountGroups                        8.827  0.125   8.999
UpdateNodeSize                     8.799  0.016   8.837
PlotFlowSOM                        8.580  0.060   8.663
SaveClustersToFCS                  8.296  0.020   8.333
PlotLabels                         7.607  0.004   7.632
GetFeatures                        7.495  0.024   7.541
NMetaclusters                      7.144  0.028   7.193
PlotOverview2D                     7.041  0.076   7.131
MetaclusterMFIs                    7.014  0.044   7.079
TestOutliers                       6.887  0.004   6.905
NClusters                          6.725  0.020   6.764
print.FlowSOM                      6.497  0.028   6.540
GetMetaclusterCVs                  6.463  0.012   6.493
GetMetaclusterMFIs                 6.367  0.052   6.437
MetaclusterCVs                     6.403  0.008   6.438
GetPercentages                     6.366  0.036   6.420
GetClusterMFIs                     6.315  0.044   6.375
GetMetaclusters                    6.331  0.011   6.361
GetMFIs                            6.333  0.004   6.355
GetMetaclusterPercentagesPositive  6.220  0.032   6.269
FlowSOMSubset                      6.157  0.035   6.225
GetCounts                          6.013  0.015   6.044
GetClusterPercentagesPositive      6.015  0.008   6.044
GetClusters                        6.017  0.000   6.034
NewData                            5.257  0.008   5.280
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.16.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c som.c -o som.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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
AddAnnotation12.304 0.17012.515
AggregateFlowFrames0.0830.0040.087
BuildMST2.1430.0352.187
BuildSOM1.7700.0291.811
CountGroups8.8270.1258.999
FMeasure0.0020.0000.002
FlowSOM16.819 0.11116.999
FlowSOMSubset6.1570.0356.225
FlowSOMmary83.389 0.31883.781
GetChannels0.0330.0000.033
GetClusterMFIs6.3150.0446.375
GetClusterPercentagesPositive6.0150.0086.044
GetClusters6.0170.0006.034
GetCounts6.0130.0156.044
GetFeatures7.4950.0247.541
GetFlowJoLabels9.8410.0729.942
GetMFIs6.3330.0046.355
GetMarkers0.0330.0000.033
GetMetaclusterCVs6.4630.0126.493
GetMetaclusterMFIs6.3670.0526.437
GetMetaclusterPercentagesPositive6.2200.0326.269
GetMetaclusters6.3310.0116.361
GetPercentages6.3660.0366.420
GroupStats18.046 0.03918.140
Initialize_KWSP0.0060.0000.006
Initialize_PCA0.0010.0000.001
MetaClustering4.4030.0564.476
MetaclusterCVs6.4030.0086.438
MetaclusterMFIs7.0140.0447.079
NClusters6.7250.0206.764
NMetaclusters7.1440.0287.193
NewData5.2570.0085.280
Plot2DScatters13.873 0.05213.983
PlotCenters1.8520.0041.861
PlotClusters2D1.7370.0001.742
PlotDimRed80.798 0.14381.103
PlotFileScatters1.7130.0121.734
PlotFlowSOM8.5800.0608.663
PlotGroups17.013 0.01617.074
PlotLabels7.6070.0047.632
PlotManualBars12.594 0.02012.651
PlotMarker25.111 0.08825.274
PlotNode10.271 0.03610.329
PlotNumbers9.6270.0169.665
PlotOutliers43.899 0.09144.094
PlotOverview2D7.0410.0767.131
PlotPies10.012 0.02810.060
PlotSD3.0660.0443.119
PlotStars20.539 0.03220.613
PlotVariable9.4380.0289.491
Purity0.0010.0000.001
QueryMultiple13.678 0.02813.738
QueryStarPlot10.046 0.02010.084
ReadInput4.7100.0484.766
SaveClustersToFCS8.2960.0208.333
TestOutliers6.8870.0046.905
UpdateMetaclusters23.889 0.14324.094
UpdateNodeSize8.7990.0168.837
get_channels0.0280.0040.032
get_markers0.0320.0000.032
metaClustering_consensus3.7600.0603.828
plotStarLegend0.6060.0080.615
print.FlowSOM6.4970.0286.540
query_multiple14.025 0.03214.091