Sofie Van Gassen
| Snapshot Date: 2026-05-08 13:45 -0400 (Fri, 08 May 2026) |
| git_url: https://git.bioconductor.org/packages/FlowSOM |
| git_branch: devel |
| git_last_commit: 5975471 |
| git_last_commit_date: 2026-04-28 08:40:20 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-09 15:11 -0400 (Sat, 09 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4890 |
| 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 771/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BIOCCHECK | BUILD BIN | ||||||||
| FlowSOM 2.21.0 (landing page) Sofie Van Gassen
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | 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: 2.21.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings FlowSOM_2.21.0.tar.gz |
| StartedAt: 2026-05-08 23:53:06 -0400 (Fri, 08 May 2026) |
| EndedAt: 2026-05-09 00:04:19 -0400 (Sat, 09 May 2026) |
| EllapsedTime: 672.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FlowSOM.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings FlowSOM_2.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-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: 2026-05-09 03:53:07 UTC
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.21.0’
* 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 53.382 0.542 53.618
PlotDimRed 48.136 0.164 48.225
PlotOutliers 30.425 0.146 30.571
PlotMarker 18.900 0.100 19.000
UpdateMetaclusters 16.779 0.014 16.794
PlotStars 15.465 0.060 15.525
GroupStats 12.954 0.110 13.049
FlowSOM 11.276 0.059 11.337
QueryMultiple 10.971 0.021 10.993
PlotGroups 10.920 0.023 10.944
query_multiple 10.928 0.004 10.933
Plot2DScatters 9.820 0.076 9.897
Plot1DScatters 9.099 0.010 9.098
PlotManualBars 9.016 0.065 9.081
QueryStarPlot 8.946 0.005 8.952
AddAnnotation 8.482 0.169 8.652
PlotVariable 7.957 0.012 7.969
PlotPies 7.839 0.086 7.925
GetFlowJoLabels 7.671 0.123 7.794
PlotNumbers 7.720 0.014 7.735
PlotNode 7.160 0.015 7.176
SaveClustersToFCS 6.893 0.022 6.916
UpdateNodeSize 6.529 0.005 6.534
PlotOverview2D 6.105 0.095 6.200
PlotFlowSOM 5.910 0.022 5.932
CountGroups 5.723 0.061 5.785
PlotLabels 5.514 0.057 5.572
NClusters 5.529 0.023 5.552
TestOutliers 5.542 0.009 5.552
GetFeatures 5.439 0.037 5.477
NMetaclusters 5.431 0.018 5.449
print.FlowSOM 5.287 0.023 5.310
MetaclusterMFIs 5.268 0.015 5.283
GetPercentages 5.243 0.037 5.281
PlotMFIHeatmap 5.118 0.006 5.124
* 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-3.24-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.
FlowSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL FlowSOM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘FlowSOM’ ... ** this is package ‘FlowSOM’ version ‘2.21.0’ ** 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-3.24-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-3.24-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.24-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.24-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 | 8.482 | 0.169 | 8.652 | |
| AggregateFlowFrames | 0.068 | 0.009 | 0.077 | |
| BuildMST | 1.141 | 0.011 | 1.152 | |
| BuildSOM | 1.409 | 0.012 | 1.422 | |
| CountGroups | 5.723 | 0.061 | 5.785 | |
| FMeasure | 0.002 | 0.000 | 0.002 | |
| FlowSOM | 11.276 | 0.059 | 11.337 | |
| FlowSOMSubset | 4.130 | 0.022 | 4.153 | |
| FlowSOMmary | 53.382 | 0.542 | 53.618 | |
| GetChannels | 0.027 | 0.001 | 0.028 | |
| GetClusterMFIs | 4.654 | 0.049 | 4.704 | |
| GetClusterPercentagesPositive | 4.457 | 0.019 | 4.480 | |
| GetClusters | 4.559 | 0.016 | 4.576 | |
| GetCounts | 4.476 | 0.042 | 4.520 | |
| GetFeatures | 5.439 | 0.037 | 5.477 | |
| GetFlowJoLabels | 7.671 | 0.123 | 7.794 | |
| GetMFIs | 4.628 | 0.011 | 4.640 | |
| GetMajorityLabels | 4.568 | 0.009 | 4.600 | |
| GetMarkers | 0.027 | 0.000 | 0.027 | |
| GetMetaclusterCVs | 4.803 | 0.013 | 4.817 | |
| GetMetaclusterMFIs | 4.871 | 0.010 | 4.882 | |
| GetMetaclusterPercentagesPositive | 4.572 | 0.016 | 4.589 | |
| GetMetaclusters | 4.640 | 0.010 | 4.651 | |
| GetPercentages | 5.243 | 0.037 | 5.281 | |
| GroupStats | 12.954 | 0.110 | 13.049 | |
| Initialize_KWSP | 0.004 | 0.000 | 0.004 | |
| Initialize_PCA | 0.001 | 0.000 | 0.001 | |
| MetaClustering | 2.950 | 0.034 | 2.985 | |
| MetaclusterCVs | 4.849 | 0.087 | 4.936 | |
| MetaclusterMFIs | 5.268 | 0.015 | 5.283 | |
| NClusters | 5.529 | 0.023 | 5.552 | |
| NMetaclusters | 5.431 | 0.018 | 5.449 | |
| NewData | 4.100 | 0.071 | 4.172 | |
| Plot1DScatters | 9.099 | 0.010 | 9.098 | |
| Plot2DScatters | 9.820 | 0.076 | 9.897 | |
| PlotCenters | 1.177 | 0.006 | 1.184 | |
| PlotClusters2D | 1.074 | 0.001 | 1.076 | |
| PlotDimRed | 48.136 | 0.164 | 48.225 | |
| PlotFileScatters | 1.107 | 0.002 | 1.108 | |
| PlotFlowSOM | 5.910 | 0.022 | 5.932 | |
| PlotGroups | 10.920 | 0.023 | 10.944 | |
| PlotLabels | 5.514 | 0.057 | 5.572 | |
| PlotMFIHeatmap | 5.118 | 0.006 | 5.124 | |
| PlotManualBars | 9.016 | 0.065 | 9.081 | |
| PlotMarker | 18.9 | 0.1 | 19.0 | |
| PlotNode | 7.160 | 0.015 | 7.176 | |
| PlotNumbers | 7.720 | 0.014 | 7.735 | |
| PlotOutliers | 30.425 | 0.146 | 30.571 | |
| PlotOverview2D | 6.105 | 0.095 | 6.200 | |
| PlotPies | 7.839 | 0.086 | 7.925 | |
| PlotSD | 2.112 | 0.004 | 2.116 | |
| PlotStarLegend | 0.452 | 0.001 | 0.452 | |
| PlotStars | 15.465 | 0.060 | 15.525 | |
| PlotVariable | 7.957 | 0.012 | 7.969 | |
| Purity | 0.001 | 0.000 | 0.001 | |
| QueryMultiple | 10.971 | 0.021 | 10.993 | |
| QueryStarPlot | 8.946 | 0.005 | 8.952 | |
| ReadInput | 3.157 | 0.039 | 3.197 | |
| SaveClustersToFCS | 6.893 | 0.022 | 6.916 | |
| TestOutliers | 5.542 | 0.009 | 5.552 | |
| UpdateMetaclusters | 16.779 | 0.014 | 16.794 | |
| UpdateNodeSize | 6.529 | 0.005 | 6.534 | |
| get_channels | 0.03 | 0.00 | 0.03 | |
| get_markers | 0.030 | 0.000 | 0.029 | |
| metaClustering_consensus | 2.705 | 0.028 | 2.733 | |
| print.FlowSOM | 5.287 | 0.023 | 5.310 | |
| query_multiple | 10.928 | 0.004 | 10.933 | |