Sofie Van Gassen
| Snapshot Date: 2026-02-23 13:40 -0500 (Mon, 23 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/FlowSOM |
| git_branch: devel |
| git_last_commit: 58b41f9 |
| git_last_commit_date: 2026-02-03 08:22:12 -0500 (Tue, 03 Feb 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-24 11:32 -0500 (Tue, 24 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4872 |
| 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 769/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FlowSOM 2.19.3 (landing page) Sofie Van Gassen
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| 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: 2.19.3 |
| 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_2.19.3.tar.gz |
| StartedAt: 2026-02-23 23:46:34 -0500 (Mon, 23 Feb 2026) |
| EndedAt: 2026-02-23 23:57:50 -0500 (Mon, 23 Feb 2026) |
| EllapsedTime: 675.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: FlowSOM.Rcheck |
| Warnings: 1 |
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### Running command:
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### /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_2.19.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘2.19.3’
* 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 ... WARNING
Found the following significant warnings:
/home/biocbuild/bbs-3.23-bioc/R/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
See ‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck/00install.out’ for details.
* 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 ... 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 54.162 0.531 54.341
PlotDimRed 44.036 0.136 44.104
PlotOutliers 29.969 0.099 30.068
PlotMarker 20.094 0.096 20.190
PlotStars 17.381 0.027 18.056
UpdateMetaclusters 16.817 0.022 16.840
GroupStats 14.068 0.085 14.143
PlotGroups 12.079 0.039 12.117
FlowSOM 11.865 0.049 11.915
Plot2DScatters 11.055 0.075 11.132
QueryMultiple 10.173 0.037 10.211
Plot1DScatters 9.936 0.011 9.930
query_multiple 9.783 0.009 9.792
PlotManualBars 9.177 0.019 9.196
AddAnnotation 8.198 0.142 8.343
QueryStarPlot 8.239 0.010 8.249
GetClusterPercentagesPositive 7.993 0.025 9.142
PlotNode 7.883 0.065 7.949
PlotNumbers 7.840 0.016 7.856
GetFlowJoLabels 7.649 0.045 7.699
PlotVariable 7.427 0.016 7.444
PlotPies 7.225 0.051 7.275
PlotOverview2D 6.338 0.080 6.418
PlotFlowSOM 6.328 0.038 6.366
GetFeatures 6.308 0.011 6.319
PlotLabels 5.954 0.046 6.000
UpdateNodeSize 5.920 0.007 5.927
SaveClustersToFCS 5.893 0.009 5.903
NMetaclusters 5.798 0.008 5.806
GetPercentages 5.716 0.021 5.738
CountGroups 5.673 0.049 5.721
TestOutliers 5.655 0.009 5.664
GetMajorityLabels 5.542 0.012 5.556
MetaclusterMFIs 5.544 0.007 5.551
PlotMFIHeatmap 5.410 0.034 5.444
NClusters 5.336 0.007 5.343
GetMetaclusterCVs 5.228 0.071 5.300
GetMFIs 5.285 0.011 5.299
GetMetaclusters 5.161 0.040 5.201
GetMetaclusterPercentagesPositive 4.989 0.046 5.035
GetMetaclusterMFIs 5.024 0.007 5.031
* 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 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.
FlowSOM.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.19.3’
** 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-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c som.c -o som.o
In file included from som.c:11:
/home/biocbuild/bbs-3.23-bioc/R/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
| ^~~~~~~
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 | 8.198 | 0.142 | 8.343 | |
| AggregateFlowFrames | 0.087 | 0.015 | 0.102 | |
| BuildMST | 1.442 | 0.038 | 1.480 | |
| BuildSOM | 1.124 | 0.020 | 1.143 | |
| CountGroups | 5.673 | 0.049 | 5.721 | |
| FMeasure | 0.002 | 0.000 | 0.001 | |
| FlowSOM | 11.865 | 0.049 | 11.915 | |
| FlowSOMSubset | 3.935 | 0.010 | 3.945 | |
| FlowSOMmary | 54.162 | 0.531 | 54.341 | |
| GetChannels | 0.030 | 0.000 | 0.031 | |
| GetClusterMFIs | 4.743 | 0.027 | 4.770 | |
| GetClusterPercentagesPositive | 7.993 | 0.025 | 9.142 | |
| GetClusters | 4.731 | 0.049 | 4.781 | |
| GetCounts | 4.740 | 0.049 | 4.790 | |
| GetFeatures | 6.308 | 0.011 | 6.319 | |
| GetFlowJoLabels | 7.649 | 0.045 | 7.699 | |
| GetMFIs | 5.285 | 0.011 | 5.299 | |
| GetMajorityLabels | 5.542 | 0.012 | 5.556 | |
| GetMarkers | 0.028 | 0.000 | 0.028 | |
| GetMetaclusterCVs | 5.228 | 0.071 | 5.300 | |
| GetMetaclusterMFIs | 5.024 | 0.007 | 5.031 | |
| GetMetaclusterPercentagesPositive | 4.989 | 0.046 | 5.035 | |
| GetMetaclusters | 5.161 | 0.040 | 5.201 | |
| GetPercentages | 5.716 | 0.021 | 5.738 | |
| GroupStats | 14.068 | 0.085 | 14.143 | |
| Initialize_KWSP | 0.004 | 0.000 | 0.004 | |
| Initialize_PCA | 0.001 | 0.000 | 0.001 | |
| MetaClustering | 2.955 | 0.015 | 2.970 | |
| MetaclusterCVs | 4.937 | 0.009 | 4.947 | |
| MetaclusterMFIs | 5.544 | 0.007 | 5.551 | |
| NClusters | 5.336 | 0.007 | 5.343 | |
| NMetaclusters | 5.798 | 0.008 | 5.806 | |
| NewData | 4.716 | 0.063 | 4.780 | |
| Plot1DScatters | 9.936 | 0.011 | 9.930 | |
| Plot2DScatters | 11.055 | 0.075 | 11.132 | |
| PlotCenters | 1.237 | 0.006 | 1.243 | |
| PlotClusters2D | 1.087 | 0.002 | 1.089 | |
| PlotDimRed | 44.036 | 0.136 | 44.104 | |
| PlotFileScatters | 1.110 | 0.006 | 1.116 | |
| PlotFlowSOM | 6.328 | 0.038 | 6.366 | |
| PlotGroups | 12.079 | 0.039 | 12.117 | |
| PlotLabels | 5.954 | 0.046 | 6.000 | |
| PlotMFIHeatmap | 5.410 | 0.034 | 5.444 | |
| PlotManualBars | 9.177 | 0.019 | 9.196 | |
| PlotMarker | 20.094 | 0.096 | 20.190 | |
| PlotNode | 7.883 | 0.065 | 7.949 | |
| PlotNumbers | 7.840 | 0.016 | 7.856 | |
| PlotOutliers | 29.969 | 0.099 | 30.068 | |
| PlotOverview2D | 6.338 | 0.080 | 6.418 | |
| PlotPies | 7.225 | 0.051 | 7.275 | |
| PlotSD | 2.067 | 0.013 | 2.080 | |
| PlotStarLegend | 0.445 | 0.001 | 0.445 | |
| PlotStars | 17.381 | 0.027 | 18.056 | |
| PlotVariable | 7.427 | 0.016 | 7.444 | |
| Purity | 0.001 | 0.000 | 0.001 | |
| QueryMultiple | 10.173 | 0.037 | 10.211 | |
| QueryStarPlot | 8.239 | 0.010 | 8.249 | |
| ReadInput | 3.780 | 0.014 | 3.794 | |
| SaveClustersToFCS | 5.893 | 0.009 | 5.903 | |
| TestOutliers | 5.655 | 0.009 | 5.664 | |
| UpdateMetaclusters | 16.817 | 0.022 | 16.840 | |
| UpdateNodeSize | 5.920 | 0.007 | 5.927 | |
| get_channels | 0.026 | 0.002 | 0.029 | |
| get_markers | 0.046 | 0.000 | 0.046 | |
| metaClustering_consensus | 3.060 | 0.006 | 3.066 | |
| print.FlowSOM | 4.687 | 0.007 | 4.695 | |
| query_multiple | 9.783 | 0.009 | 9.792 | |