Sofie Van Gassen
| Snapshot Date: 2026-05-11 13:40 -0400 (Mon, 11 May 2026) |
| git_url: https://git.bioconductor.org/packages/FlowSOM |
| git_branch: RELEASE_3_23 |
| git_last_commit: 80480d4 |
| git_last_commit_date: 2026-04-28 08:40:20 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-12 11:36 -0400 (Tue, 12 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4994 |
| 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 781/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FlowSOM 2.20.0 (landing page) Sofie Van Gassen
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for FlowSOM in R Universe. | ||||||||||||||
|
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. |
| Package: FlowSOM |
| Version: 2.20.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings FlowSOM_2.20.0.tar.gz |
| StartedAt: 2026-05-12 00:07:05 -0400 (Tue, 12 May 2026) |
| EndedAt: 2026-05-12 00:18:34 -0400 (Tue, 12 May 2026) |
| EllapsedTime: 689.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FlowSOM.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings FlowSOM_2.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-12 04:07:05 UTC
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.20.0’
* 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 13.3.0-6ubuntu2~24.04.1) 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 ... OK
* 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
FlowSOMmary 55.395 0.345 55.385
PlotDimRed 49.245 0.255 50.613
PlotOutliers 29.387 0.258 29.645
PlotMarker 18.713 0.288 19.001
UpdateMetaclusters 17.898 0.018 17.919
PlotStars 16.068 0.111 16.179
GroupStats 13.831 0.074 13.884
PlotGroups 11.525 0.444 11.969
FlowSOM 11.846 0.056 11.903
QueryMultiple 11.091 0.117 11.208
query_multiple 10.788 0.072 10.861
Plot2DScatters 10.735 0.052 10.789
Plot1DScatters 9.354 0.064 9.403
AddAnnotation 8.914 0.159 9.075
PlotManualBars 8.744 0.210 8.955
QueryStarPlot 8.181 0.019 8.200
PlotPies 7.804 0.092 7.897
GetFlowJoLabels 7.705 0.095 7.801
PlotNode 7.616 0.182 7.799
PlotVariable 7.602 0.084 7.685
PlotNumbers 7.567 0.038 7.606
PlotFlowSOM 6.401 0.411 6.825
PlotOverview2D 6.265 0.140 6.404
UpdateNodeSize 6.120 0.009 6.130
CountGroups 5.854 0.117 5.972
PlotLabels 5.789 0.173 5.962
SaveClustersToFCS 5.936 0.017 5.954
MetaclusterMFIs 5.847 0.017 5.865
PlotMFIHeatmap 5.701 0.141 5.842
GetMajorityLabels 5.650 0.016 5.668
TestOutliers 5.534 0.013 5.549
GetFeatures 5.526 0.008 5.534
NClusters 5.362 0.007 5.369
print.FlowSOM 5.306 0.041 5.348
GetPercentages 5.313 0.017 5.330
GetMFIs 5.126 0.087 5.213
GetMetaclusterPercentagesPositive 5.192 0.020 5.212
GetMetaclusterMFIs 5.136 0.010 5.148
GetMetaclusterCVs 5.028 0.008 5.037
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.
FlowSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL FlowSOM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘FlowSOM’ ... ** this is package ‘FlowSOM’ version ‘2.20.0’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-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-3.23-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-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)
FlowSOM.Rcheck/FlowSOM-Ex.timings
| name | user | system | elapsed | |
| AddAnnotation | 8.914 | 0.159 | 9.075 | |
| AggregateFlowFrames | 0.080 | 0.009 | 0.089 | |
| BuildMST | 1.395 | 0.027 | 1.423 | |
| BuildSOM | 1.375 | 0.004 | 1.378 | |
| CountGroups | 5.854 | 0.117 | 5.972 | |
| FMeasure | 0.002 | 0.000 | 0.001 | |
| FlowSOM | 11.846 | 0.056 | 11.903 | |
| FlowSOMSubset | 4.289 | 0.021 | 4.310 | |
| FlowSOMmary | 55.395 | 0.345 | 55.385 | |
| GetChannels | 0.030 | 0.001 | 0.032 | |
| GetClusterMFIs | 4.936 | 0.058 | 4.995 | |
| GetClusterPercentagesPositive | 4.648 | 0.007 | 4.656 | |
| GetClusters | 4.561 | 0.055 | 4.616 | |
| GetCounts | 4.712 | 0.009 | 4.721 | |
| GetFeatures | 5.526 | 0.008 | 5.534 | |
| GetFlowJoLabels | 7.705 | 0.095 | 7.801 | |
| GetMFIs | 5.126 | 0.087 | 5.213 | |
| GetMajorityLabels | 5.650 | 0.016 | 5.668 | |
| GetMarkers | 0.027 | 0.000 | 0.027 | |
| GetMetaclusterCVs | 5.028 | 0.008 | 5.037 | |
| GetMetaclusterMFIs | 5.136 | 0.010 | 5.148 | |
| GetMetaclusterPercentagesPositive | 5.192 | 0.020 | 5.212 | |
| GetMetaclusters | 4.864 | 0.030 | 4.895 | |
| GetPercentages | 5.313 | 0.017 | 5.330 | |
| GroupStats | 13.831 | 0.074 | 13.884 | |
| Initialize_KWSP | 0.004 | 0.000 | 0.004 | |
| Initialize_PCA | 0.001 | 0.000 | 0.001 | |
| MetaClustering | 2.884 | 0.012 | 2.898 | |
| MetaclusterCVs | 4.713 | 0.007 | 4.722 | |
| MetaclusterMFIs | 5.847 | 0.017 | 5.865 | |
| NClusters | 5.362 | 0.007 | 5.369 | |
| NMetaclusters | 4.788 | 0.052 | 4.841 | |
| NewData | 4.160 | 0.026 | 4.186 | |
| Plot1DScatters | 9.354 | 0.064 | 9.403 | |
| Plot2DScatters | 10.735 | 0.052 | 10.789 | |
| PlotCenters | 1.199 | 0.021 | 1.220 | |
| PlotClusters2D | 1.111 | 0.003 | 1.114 | |
| PlotDimRed | 49.245 | 0.255 | 50.613 | |
| PlotFileScatters | 1.195 | 0.089 | 1.284 | |
| PlotFlowSOM | 6.401 | 0.411 | 6.825 | |
| PlotGroups | 11.525 | 0.444 | 11.969 | |
| PlotLabels | 5.789 | 0.173 | 5.962 | |
| PlotMFIHeatmap | 5.701 | 0.141 | 5.842 | |
| PlotManualBars | 8.744 | 0.210 | 8.955 | |
| PlotMarker | 18.713 | 0.288 | 19.001 | |
| PlotNode | 7.616 | 0.182 | 7.799 | |
| PlotNumbers | 7.567 | 0.038 | 7.606 | |
| PlotOutliers | 29.387 | 0.258 | 29.645 | |
| PlotOverview2D | 6.265 | 0.140 | 6.404 | |
| PlotPies | 7.804 | 0.092 | 7.897 | |
| PlotSD | 2.136 | 0.025 | 2.162 | |
| PlotStarLegend | 0.474 | 0.002 | 0.476 | |
| PlotStars | 16.068 | 0.111 | 16.179 | |
| PlotVariable | 7.602 | 0.084 | 7.685 | |
| Purity | 0.002 | 0.000 | 0.001 | |
| QueryMultiple | 11.091 | 0.117 | 11.208 | |
| QueryStarPlot | 8.181 | 0.019 | 8.200 | |
| ReadInput | 3.142 | 0.054 | 3.197 | |
| SaveClustersToFCS | 5.936 | 0.017 | 5.954 | |
| TestOutliers | 5.534 | 0.013 | 5.549 | |
| UpdateMetaclusters | 17.898 | 0.018 | 17.919 | |
| UpdateNodeSize | 6.120 | 0.009 | 6.130 | |
| get_channels | 0.026 | 0.002 | 0.028 | |
| get_markers | 0.040 | 0.004 | 0.043 | |
| metaClustering_consensus | 2.559 | 0.049 | 2.608 | |
| print.FlowSOM | 5.306 | 0.041 | 5.348 | |
| query_multiple | 10.788 | 0.072 | 10.861 | |