Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-02 11:38 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4831
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4612
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4584
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: 2025-09-29 13:40 -0400 (Mon, 29 Sep 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 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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 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: 2.16.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings FlowSOM_2.16.0.tar.gz
StartedAt: 2025-10-01 23:20:12 -0400 (Wed, 01 Oct 2025)
EndedAt: 2025-10-01 23:30:15 -0400 (Wed, 01 Oct 2025)
EllapsedTime: 602.9 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings FlowSOM_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘2.16.0’
* 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: ‘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        50.877  0.521  51.224
PlotDimRed         44.572  0.218  44.806
PlotOutliers       29.434  0.076  29.511
PlotMarker         17.211  0.041  17.255
UpdateMetaclusters 16.763  0.021  16.785
PlotStars          13.798  0.011  13.811
FlowSOM            12.270  0.044  12.316
GroupStats         12.283  0.028  12.312
PlotGroups         11.103  0.031  11.135
QueryMultiple       9.631  0.007   9.639
Plot2DScatters      9.518  0.063   9.572
query_multiple      9.048  0.008   9.056
AddAnnotation       8.618  0.210   8.830
PlotManualBars      7.760  0.007   7.769
QueryStarPlot       7.295  0.009   7.306
GetFlowJoLabels     7.223  0.067   7.338
PlotNode            7.031  0.050   7.082
PlotPies            6.773  0.064   6.837
PlotNumbers         6.266  0.032   6.298
PlotVariable        6.200  0.011   6.213
PlotFlowSOM         5.704  0.061   5.766
CountGroups         5.700  0.043   5.744
PlotOverview2D      5.507  0.149   5.656
UpdateNodeSize      5.629  0.003   5.632
SaveClustersToFCS   5.330  0.032   5.362
MetaclusterMFIs     5.161  0.028   5.190
GetFeatures         5.012  0.009   5.021
PlotLabels          4.985  0.018   5.003
* 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-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.16.0’
** 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-3.21-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-3.21-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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
AddAnnotation8.6180.2108.830
AggregateFlowFrames0.0720.0060.079
BuildMST1.3500.0281.377
BuildSOM1.0440.0121.056
CountGroups5.7000.0435.744
FMeasure0.0010.0010.002
FlowSOM12.270 0.04412.316
FlowSOMSubset4.2210.0234.245
FlowSOMmary50.877 0.52151.224
GetChannels0.0260.0020.028
GetClusterMFIs4.4300.0844.515
GetClusterPercentagesPositive3.9790.0454.024
GetClusters3.9980.0694.067
GetCounts3.8610.0493.910
GetFeatures5.0120.0095.021
GetFlowJoLabels7.2230.0677.338
GetMFIs4.1060.0174.123
GetMarkers0.0270.0000.027
GetMetaclusterCVs4.6570.0124.670
GetMetaclusterMFIs4.4620.0214.484
GetMetaclusterPercentagesPositive4.6770.0174.695
GetMetaclusters4.3320.0204.352
GetPercentages4.3330.0254.358
GroupStats12.283 0.02812.312
Initialize_KWSP0.0040.0000.004
Initialize_PCA0.0010.0000.001
MetaClustering2.6930.0252.718
MetaclusterCVs4.0710.0104.081
MetaclusterMFIs5.1610.0285.190
NClusters4.7490.0174.767
NMetaclusters4.7810.0154.796
NewData3.9960.0114.007
Plot2DScatters9.5180.0639.572
PlotCenters1.060.011.07
PlotClusters2D0.9760.0040.980
PlotDimRed44.572 0.21844.806
PlotFileScatters1.0970.0181.115
PlotFlowSOM5.7040.0615.766
PlotGroups11.103 0.03111.135
PlotLabels4.9850.0185.003
PlotManualBars7.7600.0077.769
PlotMarker17.211 0.04117.255
PlotNode7.0310.0507.082
PlotNumbers6.2660.0326.298
PlotOutliers29.434 0.07629.511
PlotOverview2D5.5070.1495.656
PlotPies6.7730.0646.837
PlotSD1.8940.0171.910
PlotStars13.798 0.01113.811
PlotVariable6.2000.0116.213
Purity0.0010.0000.001
QueryMultiple9.6310.0079.639
QueryStarPlot7.2950.0097.306
ReadInput2.9060.0612.966
SaveClustersToFCS5.3300.0325.362
TestOutliers4.8510.0064.857
UpdateMetaclusters16.763 0.02116.785
UpdateNodeSize5.6290.0035.632
get_channels0.0270.0000.027
get_markers0.0270.0000.028
metaClustering_consensus2.2320.0262.258
plotStarLegend0.4550.0010.456
print.FlowSOM3.9820.0133.995
query_multiple9.0480.0089.056