Sofie Van Gassen
| Snapshot Date: 2026-04-26 13:40 -0400 (Sun, 26 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/FlowSOM |
| git_branch: devel |
| git_last_commit: b2d43e0 |
| git_last_commit_date: 2026-03-17 05:41:52 -0400 (Tue, 17 Mar 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-27 11:32 -0400 (Mon, 27 Apr 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" | 4980 |
| 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 781/2417 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FlowSOM 2.19.4 (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: 2.19.4 |
| 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_2.19.4.tar.gz |
| StartedAt: 2026-04-27 00:06:18 -0400 (Mon, 27 Apr 2026) |
| EndedAt: 2026-04-27 00:17:36 -0400 (Mon, 27 Apr 2026) |
| EllapsedTime: 678.0 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_2.19.4.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: 2026-04-27 04:06:18 UTC
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.19.4’
* 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 58.120 0.643 59.914
PlotDimRed 45.629 0.133 45.750
PlotOutliers 33.321 0.214 33.618
PlotMarker 19.034 0.028 19.062
UpdateMetaclusters 16.422 0.037 16.460
PlotStars 14.425 0.057 14.483
GroupStats 13.050 0.050 13.079
FlowSOM 11.712 0.041 11.754
PlotGroups 11.274 0.043 11.342
QueryMultiple 10.582 0.026 10.608
query_multiple 10.080 0.011 10.091
Plot2DScatters 10.054 0.019 10.073
Plot1DScatters 9.321 0.059 9.361
PlotManualBars 8.511 0.010 8.522
AddAnnotation 8.374 0.138 8.516
QueryStarPlot 8.188 0.021 8.210
PlotNode 8.074 0.087 8.160
GetFlowJoLabels 7.933 0.073 8.007
PlotNumbers 7.364 0.011 7.376
PlotPies 7.300 0.053 7.353
PlotVariable 7.316 0.009 7.325
PlotOverview2D 6.468 0.067 6.536
GetFeatures 6.202 0.030 6.233
PlotFlowSOM 6.114 0.061 6.175
CountGroups 6.121 0.043 6.163
PlotLabels 6.145 0.006 6.151
NMetaclusters 5.958 0.076 6.035
UpdateNodeSize 5.999 0.018 6.016
SaveClustersToFCS 5.704 0.012 5.716
PlotMFIHeatmap 5.653 0.007 5.660
GetMetaclusterCVs 5.529 0.020 5.549
GetMetaclusterPercentagesPositive 5.478 0.010 5.488
GetMFIs 5.455 0.011 5.466
TestOutliers 5.401 0.009 5.424
GetMajorityLabels 5.316 0.006 5.324
NClusters 5.208 0.003 5.214
GetMetaclusterMFIs 5.179 0.007 5.187
GetCounts 5.135 0.014 5.150
MetaclusterMFIs 5.087 0.011 5.100
MetaclusterCVs 4.999 0.057 5.056
GetPercentages 5.031 0.009 5.041
GetMetaclusters 5.013 0.008 5.022
* 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 ‘2.19.4’ ** 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 | 8.374 | 0.138 | 8.516 | |
| AggregateFlowFrames | 0.086 | 0.016 | 0.102 | |
| BuildMST | 1.493 | 0.037 | 1.530 | |
| BuildSOM | 1.441 | 0.019 | 1.460 | |
| CountGroups | 6.121 | 0.043 | 6.163 | |
| FMeasure | 0.001 | 0.001 | 0.001 | |
| FlowSOM | 11.712 | 0.041 | 11.754 | |
| FlowSOMSubset | 4.521 | 0.024 | 4.546 | |
| FlowSOMmary | 58.120 | 0.643 | 59.914 | |
| GetChannels | 0.029 | 0.002 | 0.030 | |
| GetClusterMFIs | 4.725 | 0.046 | 4.770 | |
| GetClusterPercentagesPositive | 4.760 | 0.024 | 4.784 | |
| GetClusters | 4.840 | 0.034 | 4.875 | |
| GetCounts | 5.135 | 0.014 | 5.150 | |
| GetFeatures | 6.202 | 0.030 | 6.233 | |
| GetFlowJoLabels | 7.933 | 0.073 | 8.007 | |
| GetMFIs | 5.455 | 0.011 | 5.466 | |
| GetMajorityLabels | 5.316 | 0.006 | 5.324 | |
| GetMarkers | 0.040 | 0.003 | 0.043 | |
| GetMetaclusterCVs | 5.529 | 0.020 | 5.549 | |
| GetMetaclusterMFIs | 5.179 | 0.007 | 5.187 | |
| GetMetaclusterPercentagesPositive | 5.478 | 0.010 | 5.488 | |
| GetMetaclusters | 5.013 | 0.008 | 5.022 | |
| GetPercentages | 5.031 | 0.009 | 5.041 | |
| GroupStats | 13.050 | 0.050 | 13.079 | |
| Initialize_KWSP | 0.003 | 0.000 | 0.004 | |
| Initialize_PCA | 0.001 | 0.000 | 0.001 | |
| MetaClustering | 3.008 | 0.016 | 3.024 | |
| MetaclusterCVs | 4.999 | 0.057 | 5.056 | |
| MetaclusterMFIs | 5.087 | 0.011 | 5.100 | |
| NClusters | 5.208 | 0.003 | 5.214 | |
| NMetaclusters | 5.958 | 0.076 | 6.035 | |
| NewData | 4.255 | 0.010 | 4.270 | |
| Plot1DScatters | 9.321 | 0.059 | 9.361 | |
| Plot2DScatters | 10.054 | 0.019 | 10.073 | |
| PlotCenters | 1.156 | 0.002 | 1.158 | |
| PlotClusters2D | 1.088 | 0.012 | 1.100 | |
| PlotDimRed | 45.629 | 0.133 | 45.750 | |
| PlotFileScatters | 1.130 | 0.029 | 1.160 | |
| PlotFlowSOM | 6.114 | 0.061 | 6.175 | |
| PlotGroups | 11.274 | 0.043 | 11.342 | |
| PlotLabels | 6.145 | 0.006 | 6.151 | |
| PlotMFIHeatmap | 5.653 | 0.007 | 5.660 | |
| PlotManualBars | 8.511 | 0.010 | 8.522 | |
| PlotMarker | 19.034 | 0.028 | 19.062 | |
| PlotNode | 8.074 | 0.087 | 8.160 | |
| PlotNumbers | 7.364 | 0.011 | 7.376 | |
| PlotOutliers | 33.321 | 0.214 | 33.618 | |
| PlotOverview2D | 6.468 | 0.067 | 6.536 | |
| PlotPies | 7.300 | 0.053 | 7.353 | |
| PlotSD | 2.646 | 0.010 | 2.656 | |
| PlotStarLegend | 0.439 | 0.002 | 0.440 | |
| PlotStars | 14.425 | 0.057 | 14.483 | |
| PlotVariable | 7.316 | 0.009 | 7.325 | |
| Purity | 0.001 | 0.000 | 0.001 | |
| QueryMultiple | 10.582 | 0.026 | 10.608 | |
| QueryStarPlot | 8.188 | 0.021 | 8.210 | |
| ReadInput | 3.704 | 0.038 | 3.742 | |
| SaveClustersToFCS | 5.704 | 0.012 | 5.716 | |
| TestOutliers | 5.401 | 0.009 | 5.424 | |
| UpdateMetaclusters | 16.422 | 0.037 | 16.460 | |
| UpdateNodeSize | 5.999 | 0.018 | 6.016 | |
| get_channels | 0.027 | 0.000 | 0.028 | |
| get_markers | 0.026 | 0.002 | 0.028 | |
| metaClustering_consensus | 2.776 | 0.025 | 2.802 | |
| print.FlowSOM | 4.970 | 0.017 | 4.988 | |
| query_multiple | 10.080 | 0.011 | 10.091 | |