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This page was generated on 2025-10-03 12:07 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
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: 2025-10-02 13:45 -0400 (Thu, 02 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 12.7.1 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 taishan

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: 2.17.0
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_2.17.0.tar.gz
StartedAt: 2025-10-03 07:13:18 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 07:25:03 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 705.0 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_2.17.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* 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: ‘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                       73.732  0.279  74.139
PlotDimRed                        71.179  0.175  71.503
PlotOutliers                      42.701  0.124  42.952
PlotMarker                        23.330  0.099  23.492
UpdateMetaclusters                22.353  0.134  22.546
PlotStars                         18.872  0.032  18.951
GroupStats                        16.321  0.107  16.472
FlowSOM                           15.617  0.039  15.700
PlotGroups                        15.228  0.020  15.296
QueryMultiple                     13.363  0.048  13.442
query_multiple                    13.079  0.016  13.131
Plot2DScatters                    12.706  0.040  12.785
AddAnnotation                     11.873  0.088  11.995
PlotManualBars                    11.620  0.028  11.677
QueryStarPlot                      9.873  0.024   9.922
GetFlowJoLabels                    9.180  0.115   9.328
PlotNumbers                        9.129  0.032   9.183
PlotNode                           9.023  0.028   9.074
PlotPies                           8.895  0.071   8.995
UpdateNodeSize                     8.699  0.025   8.746
PlotVariable                       8.364  0.024   8.409
CountGroups                        8.047  0.028   8.094
PlotFlowSOM                        7.618  0.088   7.730
GetFeatures                        7.192  0.060   7.271
PlotLabels                         7.165  0.016   7.199
SaveClustersToFCS                  6.930  0.020   6.969
PlotOverview2D                     6.386  0.080   6.485
MetaclusterMFIs                    6.204  0.028   6.249
TestOutliers                       6.202  0.016   6.236
NMetaclusters                      6.161  0.044   6.223
NClusters                          6.158  0.000   6.177
MetaclusterCVs                     6.012  0.012   6.041
GetMFIs                            5.903  0.088   6.007
GetMetaclusters                    5.669  0.056   5.738
GetMetaclusterCVs                  5.548  0.076   5.636
print.FlowSOM                      5.568  0.032   5.614
GetPercentages                     5.518  0.044   5.574
FlowSOMSubset                      5.537  0.024   5.576
GetMetaclusterMFIs                 5.480  0.036   5.528
GetMetaclusterPercentagesPositive  5.422  0.036   5.469
GetCounts                          5.299  0.072   5.384
GetClusterPercentagesPositive      5.273  0.008   5.293
GetClusterMFIs                     5.189  0.088   5.290
GetClusters                        5.204  0.012   5.227
* 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-3.22-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.17.0’
** 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-4.5.0/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-4.5.0/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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
AddAnnotation11.873 0.08811.995
AggregateFlowFrames0.0780.0040.082
BuildMST2.0150.0122.033
BuildSOM1.6980.0121.714
CountGroups8.0470.0288.094
FMeasure0.0020.0000.002
FlowSOM15.617 0.03915.700
FlowSOMSubset5.5370.0245.576
FlowSOMmary73.732 0.27974.139
GetChannels0.0320.0000.031
GetClusterMFIs5.1890.0885.290
GetClusterPercentagesPositive5.2730.0085.293
GetClusters5.2040.0125.227
GetCounts5.2990.0725.384
GetFeatures7.1920.0607.271
GetFlowJoLabels9.1800.1159.328
GetMFIs5.9030.0886.007
GetMarkers0.0310.0000.030
GetMetaclusterCVs5.5480.0765.636
GetMetaclusterMFIs5.4800.0365.528
GetMetaclusterPercentagesPositive5.4220.0365.469
GetMetaclusters5.6690.0565.738
GetPercentages5.5180.0445.574
GroupStats16.321 0.10716.472
Initialize_KWSP0.0060.0000.006
Initialize_PCA0.0010.0000.001
MetaClustering4.1590.0444.216
MetaclusterCVs6.0120.0126.041
MetaclusterMFIs6.2040.0286.249
NClusters6.1580.0006.177
NMetaclusters6.1610.0446.223
NewData4.5550.0484.616
Plot2DScatters12.706 0.04012.785
PlotCenters1.7700.0241.799
PlotClusters2D1.6230.0001.628
PlotDimRed71.179 0.17571.503
PlotFileScatters1.5710.0201.596
PlotFlowSOM7.6180.0887.730
PlotGroups15.228 0.02015.296
PlotLabels7.1650.0167.199
PlotManualBars11.620 0.02811.677
PlotMarker23.330 0.09923.492
PlotNode9.0230.0289.074
PlotNumbers9.1290.0329.183
PlotOutliers42.701 0.12442.952
PlotOverview2D6.3860.0806.485
PlotPies8.8950.0718.995
PlotSD2.8590.0162.882
PlotStars18.872 0.03218.951
PlotVariable8.3640.0248.409
Purity0.0010.0000.001
QueryMultiple13.363 0.04813.442
QueryStarPlot9.8730.0249.922
ReadInput4.2960.0644.371
SaveClustersToFCS6.9300.0206.969
TestOutliers6.2020.0166.236
UpdateMetaclusters22.353 0.13422.546
UpdateNodeSize8.6990.0258.746
get_channels0.0280.0040.032
get_markers0.0320.0000.031
metaClustering_consensus3.3500.0563.413
plotStarLegend0.6000.0000.601
print.FlowSOM5.5680.0325.614
query_multiple13.079 0.01613.131