Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-09-04 11:38 -0400 (Thu, 04 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-09-01 13:40 -0400 (Mon, 01 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    NA  


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: 2025-09-03 23:12:03 -0400 (Wed, 03 Sep 2025)
EndedAt: 2025-09-03 23:21:18 -0400 (Wed, 03 Sep 2025)
EllapsedTime: 555.8 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        46.813  0.495  47.109
PlotDimRed         43.774  0.112  43.833
PlotOutliers       16.930  0.008  16.939
UpdateMetaclusters 16.012  0.025  16.038
PlotMarker         15.411  0.070  15.502
PlotStars          12.532  0.039  12.572
GroupStats         11.838  0.019  11.858
FlowSOM            10.497  0.087  10.584
PlotGroups          9.823  0.020   9.853
QueryMultiple       8.701  0.024   8.725
query_multiple      8.118  0.010   8.127
AddAnnotation       7.934  0.165   8.100
Plot2DScatters      7.658  0.022   7.669
GetFlowJoLabels     7.242  0.136   7.379
PlotManualBars      6.859  0.018   6.879
QueryStarPlot       6.316  0.005   6.321
PlotNumbers         6.168  0.013   6.181
PlotVariable        6.108  0.067   6.176
PlotNode            6.108  0.034   6.145
PlotPies            6.030  0.053   6.084
SaveClustersToFCS   5.305  0.057   5.362
GetFeatures         5.191  0.052   5.243
UpdateNodeSize      5.215  0.003   5.219
CountGroups         5.032  0.022   5.054
* 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
AddAnnotation7.9340.1658.100
AggregateFlowFrames0.0690.0210.090
BuildMST1.3030.0471.350
BuildSOM1.0290.0081.037
CountGroups5.0320.0225.054
FMeasure0.0010.0000.001
FlowSOM10.497 0.08710.584
FlowSOMSubset4.2410.0184.260
FlowSOMmary46.813 0.49547.109
GetChannels0.0290.0000.029
GetClusterMFIs3.6810.0913.773
GetClusterPercentagesPositive4.1350.0144.148
GetClusters4.1000.0074.108
GetCounts3.6440.0123.657
GetFeatures5.1910.0525.243
GetFlowJoLabels7.2420.1367.379
GetMFIs4.1600.0184.178
GetMarkers0.0270.0020.029
GetMetaclusterCVs4.4600.0094.469
GetMetaclusterMFIs4.2040.0064.210
GetMetaclusterPercentagesPositive4.3880.0244.411
GetMetaclusters4.7240.0264.750
GetPercentages4.3430.0114.355
GroupStats11.838 0.01911.858
Initialize_KWSP0.0040.0000.004
Initialize_PCA0.0010.0000.001
MetaClustering2.6890.0202.709
MetaclusterCVs4.1530.0184.173
MetaclusterMFIs4.7240.0134.736
NClusters4.6580.0154.674
NMetaclusters4.5640.0594.624
NewData3.7390.0073.746
Plot2DScatters7.6580.0227.669
PlotCenters1.0050.0061.010
PlotClusters2D1.4030.0701.473
PlotDimRed43.774 0.11243.833
PlotFileScatters0.7110.0040.716
PlotFlowSOM4.9510.0264.978
PlotGroups9.8230.0209.853
PlotLabels4.7990.0184.817
PlotManualBars6.8590.0186.879
PlotMarker15.411 0.07015.502
PlotNode6.1080.0346.145
PlotNumbers6.1680.0136.181
PlotOutliers16.930 0.00816.939
PlotOverview2D4.2030.0074.210
PlotPies6.0300.0536.084
PlotSD1.8850.0131.898
PlotStars12.532 0.03912.572
PlotVariable6.1080.0676.176
Purity0.0010.0000.001
QueryMultiple8.7010.0248.725
QueryStarPlot6.3160.0056.321
ReadInput2.9670.0172.984
SaveClustersToFCS5.3050.0575.362
TestOutliers4.6620.0114.674
UpdateMetaclusters16.012 0.02516.038
UpdateNodeSize5.2150.0035.219
get_channels0.0280.0040.031
get_markers0.0260.0030.030
metaClustering_consensus2.3810.0172.398
plotStarLegend0.3810.0010.382
print.FlowSOM4.2620.0134.275
query_multiple8.1180.0108.127