Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-23 12:03 -0400 (Thu, 23 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4894
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4684
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4629
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: 2025-10-22 13:45 -0400 (Wed, 22 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 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: 2025-10-22 23:58:10 -0400 (Wed, 22 Oct 2025)
EndedAt: 2025-10-23 00:08:03 -0400 (Thu, 23 Oct 2025)
EllapsedTime: 593.5 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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        51.097  0.524  51.450
PlotDimRed         43.306  0.125  43.409
PlotOutliers       29.548  0.086  29.635
PlotMarker         16.572  0.073  16.646
UpdateMetaclusters 15.860  0.014  15.875
PlotStars          13.688  0.025  13.714
GroupStats         12.176  0.036  12.212
FlowSOM            10.915  0.140  11.056
PlotGroups         10.756  0.009  10.765
query_multiple      9.446  0.010   9.458
QueryMultiple       9.358  0.015   9.374
Plot2DScatters      9.218  0.075   9.284
AddAnnotation       8.836  0.394   9.232
PlotManualBars      7.861  0.010   7.872
PlotNumbers         7.188  0.040   7.229
PlotNode            7.013  0.027   7.040
QueryStarPlot       6.961  0.004   6.966
GetFlowJoLabels     6.730  0.024   6.755
PlotPies            6.600  0.018   6.619
PlotVariable        6.325  0.012   6.338
UpdateNodeSize      5.784  0.004   5.788
PlotOverview2D      5.381  0.128   5.509
PlotFlowSOM         5.162  0.053   5.216
CountGroups         5.116  0.081   5.198
* 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

##############################################################################
##############################################################################
###
### 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
AddAnnotation8.8360.3949.232
AggregateFlowFrames0.0670.0070.074
BuildMST1.0080.0241.031
BuildSOM1.0520.0431.097
CountGroups5.1160.0815.198
FMeasure0.0010.0000.002
FlowSOM10.915 0.14011.056
FlowSOMSubset3.8680.0233.892
FlowSOMmary51.097 0.52451.450
GetChannels0.0260.0000.027
GetClusterMFIs3.8470.1243.971
GetClusterPercentagesPositive3.7410.0203.762
GetClusters4.0020.0184.021
GetCounts3.9030.0223.925
GetFeatures4.8610.0124.873
GetFlowJoLabels6.7300.0246.755
GetMFIs4.0530.0084.061
GetMarkers0.0280.0000.028
GetMetaclusterCVs4.1510.0044.157
GetMetaclusterMFIs4.1770.0104.188
GetMetaclusterPercentagesPositive4.3240.0484.373
GetMetaclusters4.3850.0264.412
GetPercentages4.2790.0534.332
GroupStats12.176 0.03612.212
Initialize_KWSP0.0030.0000.004
Initialize_PCA0.0010.0000.001
MetaClustering2.7880.0192.808
MetaclusterCVs4.0060.0074.014
MetaclusterMFIs4.3260.0104.337
NClusters4.2030.0624.266
NMetaclusters4.3120.0344.346
NewData3.8700.0043.876
Plot2DScatters9.2180.0759.284
PlotCenters1.0430.0011.044
PlotClusters2D0.9630.0000.963
PlotDimRed43.306 0.12543.409
PlotFileScatters1.0560.0091.065
PlotFlowSOM5.1620.0535.216
PlotGroups10.756 0.00910.765
PlotLabels4.8510.0154.866
PlotManualBars7.8610.0107.872
PlotMarker16.572 0.07316.646
PlotNode7.0130.0277.040
PlotNumbers7.1880.0407.229
PlotOutliers29.548 0.08629.635
PlotOverview2D5.3810.1285.509
PlotPies6.6000.0186.619
PlotSD2.4730.0122.485
PlotStars13.688 0.02513.714
PlotVariable6.3250.0126.338
Purity0.0000.0000.001
QueryMultiple9.3580.0159.374
QueryStarPlot6.9610.0046.966
ReadInput2.8410.0322.874
SaveClustersToFCS4.8010.0104.811
TestOutliers4.9040.0054.909
UpdateMetaclusters15.860 0.01415.875
UpdateNodeSize5.7840.0045.788
get_channels0.0280.0000.028
get_markers0.0280.0000.028
metaClustering_consensus2.3460.0122.358
plotStarLegend0.4730.0000.473
print.FlowSOM4.2500.0164.267
query_multiple9.4460.0109.458