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

This page was generated on 2025-10-06 12:04 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
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 758/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.17.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2025-10-05 13:45 -0400 (Sun, 05 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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.17.0.tar.gz
StartedAt: 2025-10-05 21:34:43 -0400 (Sun, 05 Oct 2025)
EndedAt: 2025-10-05 21:45:23 -0400 (Sun, 05 Oct 2025)
EllapsedTime: 640.0 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
FlowSOMmary                       52.832  2.135  55.201
PlotDimRed                        44.143  2.632  47.446
PlotOutliers                      36.030  0.932  37.341
PlotMarker                        22.483  1.299  24.146
UpdateMetaclusters                17.999  1.368  19.602
PlotStars                         16.376  1.130  17.730
GroupStats                        14.610  1.011  15.790
FlowSOM                           13.143  1.107  14.396
PlotGroups                        12.633  1.227  14.037
Plot2DScatters                    12.327  0.948  13.499
query_multiple                    11.025  0.553  11.746
PlotManualBars                    10.342  0.887  11.382
QueryMultiple                     10.087  0.636  11.380
AddAnnotation                      9.791  0.627  10.514
QueryStarPlot                      8.518  0.608   9.792
PlotVariable                       7.976  0.819   8.900
GetFlowJoLabels                    7.942  0.586   8.604
PlotNode                           7.669  0.768   8.548
PlotNumbers                        7.277  1.092   8.599
PlotPies                           7.359  0.853   8.343
CountGroups                        6.463  0.670   7.226
UpdateNodeSize                     6.681  0.264   6.999
PlotFlowSOM                        6.038  0.758   6.919
SaveClustersToFCS                  5.601  1.066   7.190
MetaclusterMFIs                    5.813  0.845   6.753
NMetaclusters                      5.567  0.865   6.546
GetFeatures                        5.991  0.401   6.459
PlotLabels                         5.630  0.706   6.417
PlotOverview2D                     5.522  0.636   6.252
NClusters                          5.278  0.784   6.213
MetaclusterCVs                     5.335  0.697   6.116
print.FlowSOM                      5.076  0.763   5.951
GetMetaclusters                    5.053  0.673   5.794
GetMetaclusterMFIs                 4.861  0.688   5.661
GetMetaclusterPercentagesPositive  4.776  0.689   5.567
TestOutliers                       4.749  0.675   5.496
GetMetaclusterCVs                  4.752  0.656   5.471
GetPercentages                     4.747  0.602   5.405
GetMFIs                            4.624  0.680   5.364
NewData                            4.495  0.482   5.044
* 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.17.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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
AddAnnotation 9.791 0.62710.514
AggregateFlowFrames0.0990.0060.104
BuildMST1.5130.1201.643
BuildSOM1.4600.1021.576
CountGroups6.4630.6707.226
FMeasure0.0020.0000.003
FlowSOM13.143 1.10714.396
FlowSOMSubset4.4230.4624.922
FlowSOMmary52.832 2.13555.201
GetChannels0.0420.0030.045
GetClusterMFIs4.3630.4494.876
GetClusterPercentagesPositive4.3910.4344.883
GetClusters4.3590.4724.877
GetCounts4.4560.4704.980
GetFeatures5.9910.4016.459
GetFlowJoLabels7.9420.5868.604
GetMFIs4.6240.6805.364
GetMarkers0.0430.0020.045
GetMetaclusterCVs4.7520.6565.471
GetMetaclusterMFIs4.8610.6885.661
GetMetaclusterPercentagesPositive4.7760.6895.567
GetMetaclusters5.0530.6735.794
GetPercentages4.7470.6025.405
GroupStats14.610 1.01115.790
Initialize_KWSP0.0050.0000.006
Initialize_PCA0.0010.0000.001
MetaClustering4.0280.6354.725
MetaclusterCVs5.3350.6976.116
MetaclusterMFIs5.8130.8456.753
NClusters5.2780.7846.213
NMetaclusters5.5670.8656.546
NewData4.4950.4825.044
Plot2DScatters12.327 0.94813.499
PlotCenters1.4900.0991.605
PlotClusters2D1.3720.1611.555
PlotDimRed44.143 2.63247.446
PlotFileScatters1.5130.0441.575
PlotFlowSOM6.0380.7586.919
PlotGroups12.633 1.22714.037
PlotLabels5.6300.7066.417
PlotManualBars10.342 0.88711.382
PlotMarker22.483 1.29924.146
PlotNode7.6690.7688.548
PlotNumbers7.2771.0928.599
PlotOutliers36.030 0.93237.341
PlotOverview2D5.5220.6366.252
PlotPies7.3590.8538.343
PlotSD2.5060.3132.954
PlotStars16.376 1.13017.730
PlotVariable7.9760.8198.900
Purity0.0010.0000.002
QueryMultiple10.087 0.63611.380
QueryStarPlot8.5180.6089.792
ReadInput3.4790.5704.132
SaveClustersToFCS5.6011.0667.190
TestOutliers4.7490.6755.496
UpdateMetaclusters17.999 1.36819.602
UpdateNodeSize6.6810.2646.999
get_channels0.0430.0050.051
get_markers0.0470.0020.050
metaClustering_consensus2.7150.3863.161
plotStarLegend0.5340.0050.544
print.FlowSOM5.0760.7635.951
query_multiple11.025 0.55311.746