Sofie Van Gassen
| Snapshot Date: 2026-05-22 13:40 -0400 (Fri, 22 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 2026-05-23 11:32 -0400 (Sat, 23 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" | 4995 |
| 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: 2026-05-23 00:06:28 -0400 (Sat, 23 May 2026) |
| EndedAt: 2026-05-23 00:17:46 -0400 (Sat, 23 May 2026) |
| EllapsedTime: 678.9 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: 2026-05-23 04:06:28 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 59.974 0.607 60.438
PlotDimRed 46.929 0.175 47.107
PlotOutliers 28.484 0.091 28.576
PlotMarker 18.372 0.030 18.403
UpdateMetaclusters 16.559 0.018 16.578
PlotStars 14.613 0.025 14.647
GroupStats 13.867 0.137 13.990
PlotGroups 11.804 0.027 11.833
FlowSOM 11.560 0.030 11.594
Plot2DScatters 10.616 0.065 10.680
QueryMultiple 10.530 0.035 10.565
query_multiple 9.934 0.009 9.945
PlotNumbers 9.343 0.014 10.391
Plot1DScatters 9.304 0.015 9.304
PlotManualBars 8.972 0.031 9.006
AddAnnotation 8.481 0.161 8.645
GetFlowJoLabels 8.091 0.110 8.202
QueryStarPlot 7.670 0.072 7.769
PlotNode 7.623 0.015 7.639
PlotPies 7.463 0.063 7.526
PlotVariable 7.303 0.022 7.326
PlotLabels 6.351 0.013 6.364
PlotMFIHeatmap 6.260 0.019 6.281
PlotOverview2D 6.157 0.121 6.279
PlotFlowSOM 6.183 0.025 6.208
GetMetaclusterMFIs 5.922 0.048 5.972
SaveClustersToFCS 5.827 0.035 5.862
MetaclusterMFIs 5.799 0.010 5.808
UpdateNodeSize 5.781 0.006 5.787
CountGroups 5.696 0.050 5.746
GetMajorityLabels 5.676 0.050 5.729
GetMetaclusterCVs 5.646 0.072 5.718
GetPercentages 5.614 0.046 5.660
GetFeatures 5.558 0.015 5.573
NMetaclusters 5.414 0.012 5.426
GetMetaclusters 5.397 0.014 5.411
GetMetaclusterPercentagesPositive 5.375 0.014 5.389
NClusters 5.295 0.008 5.304
TestOutliers 5.166 0.033 5.199
GetMFIs 5.030 0.008 5.040
* 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 | 8.481 | 0.161 | 8.645 | |
| AggregateFlowFrames | 0.075 | 0.017 | 0.093 | |
| BuildMST | 1.397 | 0.038 | 1.435 | |
| BuildSOM | 1.091 | 0.019 | 1.110 | |
| CountGroups | 5.696 | 0.050 | 5.746 | |
| FMeasure | 0.001 | 0.000 | 0.002 | |
| FlowSOM | 11.560 | 0.030 | 11.594 | |
| FlowSOMSubset | 4.102 | 0.019 | 4.121 | |
| FlowSOMmary | 59.974 | 0.607 | 60.438 | |
| GetChannels | 0.031 | 0.001 | 0.033 | |
| GetClusterMFIs | 4.873 | 0.057 | 4.931 | |
| GetClusterPercentagesPositive | 4.771 | 0.046 | 4.817 | |
| GetClusters | 4.620 | 0.049 | 4.669 | |
| GetCounts | 4.765 | 0.006 | 4.771 | |
| GetFeatures | 5.558 | 0.015 | 5.573 | |
| GetFlowJoLabels | 8.091 | 0.110 | 8.202 | |
| GetMFIs | 5.030 | 0.008 | 5.040 | |
| GetMajorityLabels | 5.676 | 0.050 | 5.729 | |
| GetMarkers | 0.030 | 0.012 | 0.041 | |
| GetMetaclusterCVs | 5.646 | 0.072 | 5.718 | |
| GetMetaclusterMFIs | 5.922 | 0.048 | 5.972 | |
| GetMetaclusterPercentagesPositive | 5.375 | 0.014 | 5.389 | |
| GetMetaclusters | 5.397 | 0.014 | 5.411 | |
| GetPercentages | 5.614 | 0.046 | 5.660 | |
| GroupStats | 13.867 | 0.137 | 13.990 | |
| Initialize_KWSP | 0.004 | 0.000 | 0.004 | |
| Initialize_PCA | 0.000 | 0.001 | 0.001 | |
| MetaClustering | 3.366 | 0.065 | 3.431 | |
| MetaclusterCVs | 4.843 | 0.030 | 4.873 | |
| MetaclusterMFIs | 5.799 | 0.010 | 5.808 | |
| NClusters | 5.295 | 0.008 | 5.304 | |
| NMetaclusters | 5.414 | 0.012 | 5.426 | |
| NewData | 4.230 | 0.007 | 4.240 | |
| Plot1DScatters | 9.304 | 0.015 | 9.304 | |
| Plot2DScatters | 10.616 | 0.065 | 10.680 | |
| PlotCenters | 1.16 | 0.00 | 1.16 | |
| PlotClusters2D | 1.140 | 0.036 | 1.176 | |
| PlotDimRed | 46.929 | 0.175 | 47.107 | |
| PlotFileScatters | 1.129 | 0.014 | 1.144 | |
| PlotFlowSOM | 6.183 | 0.025 | 6.208 | |
| PlotGroups | 11.804 | 0.027 | 11.833 | |
| PlotLabels | 6.351 | 0.013 | 6.364 | |
| PlotMFIHeatmap | 6.260 | 0.019 | 6.281 | |
| PlotManualBars | 8.972 | 0.031 | 9.006 | |
| PlotMarker | 18.372 | 0.030 | 18.403 | |
| PlotNode | 7.623 | 0.015 | 7.639 | |
| PlotNumbers | 9.343 | 0.014 | 10.391 | |
| PlotOutliers | 28.484 | 0.091 | 28.576 | |
| PlotOverview2D | 6.157 | 0.121 | 6.279 | |
| PlotPies | 7.463 | 0.063 | 7.526 | |
| PlotSD | 2.031 | 0.009 | 2.041 | |
| PlotStarLegend | 0.431 | 0.001 | 0.433 | |
| PlotStars | 14.613 | 0.025 | 14.647 | |
| PlotVariable | 7.303 | 0.022 | 7.326 | |
| Purity | 0.001 | 0.000 | 0.001 | |
| QueryMultiple | 10.530 | 0.035 | 10.565 | |
| QueryStarPlot | 7.670 | 0.072 | 7.769 | |
| ReadInput | 3.087 | 0.038 | 3.125 | |
| SaveClustersToFCS | 5.827 | 0.035 | 5.862 | |
| TestOutliers | 5.166 | 0.033 | 5.199 | |
| UpdateMetaclusters | 16.559 | 0.018 | 16.578 | |
| UpdateNodeSize | 5.781 | 0.006 | 5.787 | |
| get_channels | 0.039 | 0.002 | 0.041 | |
| get_markers | 0.026 | 0.002 | 0.029 | |
| metaClustering_consensus | 2.553 | 0.009 | 2.563 | |
| print.FlowSOM | 4.718 | 0.009 | 4.727 | |
| query_multiple | 9.934 | 0.009 | 9.945 | |