Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-22 12:03 -0400 (Wed, 22 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4890
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4680
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4625
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: 2025-10-21 13:45 -0400 (Tue, 21 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: 2025-10-21 23:57:06 -0400 (Tue, 21 Oct 2025)
EndedAt: 2025-10-22 00:06:45 -0400 (Wed, 22 Oct 2025)
EllapsedTime: 578.5 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        49.481  0.450  49.775
PlotDimRed         43.265  0.168  43.410
PlotOutliers       28.669  0.080  28.750
PlotMarker         16.529  0.065  16.596
UpdateMetaclusters 15.339  0.044  15.384
PlotStars          13.791  0.018  13.810
GroupStats         11.521  0.049  11.570
FlowSOM            10.553  0.022  10.576
PlotGroups         10.311  0.007  10.319
QueryMultiple       9.575  0.010   9.585
query_multiple      9.308  0.016   9.325
Plot2DScatters      9.006  0.012   9.008
AddAnnotation       8.013  0.154   8.168
PlotManualBars      7.987  0.006   7.994
QueryStarPlot       7.009  0.007   7.016
PlotPies            6.978  0.011   6.989
PlotVariable        6.922  0.016   6.939
GetFlowJoLabels     6.834  0.055   6.891
PlotNode            6.524  0.043   6.567
PlotNumbers         6.289  0.041   6.331
UpdateNodeSize      5.603  0.007   5.611
PlotFlowSOM         5.057  0.032   5.090
PlotLabels          5.004  0.007   5.011
* 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
AddAnnotation8.0130.1548.168
AggregateFlowFrames0.0650.0040.070
BuildMST0.9930.0441.036
BuildSOM1.0150.0121.027
CountGroups4.9290.0424.972
FMeasure0.0010.0000.001
FlowSOM10.553 0.02210.576
FlowSOMSubset3.7040.0163.720
FlowSOMmary49.481 0.45049.775
GetChannels0.0280.0000.028
GetClusterMFIs3.7450.1203.865
GetClusterPercentagesPositive3.8530.0293.883
GetClusters3.8110.0193.831
GetCounts3.9910.0224.014
GetFeatures4.8210.0514.873
GetFlowJoLabels6.8340.0556.891
GetMFIs3.8480.0733.922
GetMarkers0.0230.0030.027
GetMetaclusterCVs3.9480.0063.955
GetMetaclusterMFIs3.8230.0373.861
GetMetaclusterPercentagesPositive3.9110.0113.922
GetMetaclusters4.2330.0104.243
GetPercentages3.9420.0083.950
GroupStats11.521 0.04911.570
Initialize_KWSP0.0040.0000.003
Initialize_PCA0.0010.0000.001
MetaClustering2.8950.0112.906
MetaclusterCVs3.9570.0864.043
MetaclusterMFIs4.2630.0074.295
NClusters4.2690.0334.303
NMetaclusters4.3010.0114.312
NewData3.7660.0103.776
Plot2DScatters9.0060.0129.008
PlotCenters1.0190.0041.023
PlotClusters2D0.9600.0360.995
PlotDimRed43.265 0.16843.410
PlotFileScatters1.0590.0111.070
PlotFlowSOM5.0570.0325.090
PlotGroups10.311 0.00710.319
PlotLabels5.0040.0075.011
PlotManualBars7.9870.0067.994
PlotMarker16.529 0.06516.596
PlotNode6.5240.0436.567
PlotNumbers6.2890.0416.331
PlotOutliers28.669 0.08028.750
PlotOverview2D4.6440.1124.756
PlotPies6.9780.0116.989
PlotSD1.8800.0061.886
PlotStars13.791 0.01813.810
PlotVariable6.9220.0166.939
Purity0.0010.0000.001
QueryMultiple9.5750.0109.585
QueryStarPlot7.0090.0077.016
ReadInput2.8890.0152.905
SaveClustersToFCS4.7880.0164.805
TestOutliers4.4990.0114.510
UpdateMetaclusters15.339 0.04415.384
UpdateNodeSize5.6030.0075.611
get_channels0.0270.0000.027
get_markers0.0270.0000.027
metaClustering_consensus2.5810.0112.593
plotStarLegend0.4390.0010.440
print.FlowSOM4.0880.0094.099
query_multiple9.3080.0169.325