Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 756/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FlowSOM 2.16.0 (landing page) Sofie Van Gassen
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: FlowSOM |
Version: 2.16.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FlowSOM_2.16.0.tar.gz |
StartedAt: 2025-10-14 09:14:08 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 09:26:56 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 768.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FlowSOM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FlowSOM_2.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.16.0’ * 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * 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 ... NOTE checkRd: (-1) PlotDimRed.Rd:55: Lost braces 55 | of the dimred default = function(dimred){dimred$Y}.} | ^ * 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 ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed FlowSOMmary 83.389 0.318 83.781 PlotDimRed 80.798 0.143 81.103 PlotOutliers 43.899 0.091 44.094 PlotMarker 25.111 0.088 25.274 UpdateMetaclusters 23.889 0.143 24.094 PlotStars 20.539 0.032 20.613 GroupStats 18.046 0.039 18.140 PlotGroups 17.013 0.016 17.074 FlowSOM 16.819 0.111 16.999 query_multiple 14.025 0.032 14.091 Plot2DScatters 13.873 0.052 13.983 QueryMultiple 13.678 0.028 13.738 PlotManualBars 12.594 0.020 12.651 AddAnnotation 12.304 0.170 12.515 PlotNode 10.271 0.036 10.329 QueryStarPlot 10.046 0.020 10.084 PlotPies 10.012 0.028 10.060 GetFlowJoLabels 9.841 0.072 9.942 PlotNumbers 9.627 0.016 9.665 PlotVariable 9.438 0.028 9.491 CountGroups 8.827 0.125 8.999 UpdateNodeSize 8.799 0.016 8.837 PlotFlowSOM 8.580 0.060 8.663 SaveClustersToFCS 8.296 0.020 8.333 PlotLabels 7.607 0.004 7.632 GetFeatures 7.495 0.024 7.541 NMetaclusters 7.144 0.028 7.193 PlotOverview2D 7.041 0.076 7.131 MetaclusterMFIs 7.014 0.044 7.079 TestOutliers 6.887 0.004 6.905 NClusters 6.725 0.020 6.764 print.FlowSOM 6.497 0.028 6.540 GetMetaclusterCVs 6.463 0.012 6.493 GetMetaclusterMFIs 6.367 0.052 6.437 MetaclusterCVs 6.403 0.008 6.438 GetPercentages 6.366 0.036 6.420 GetClusterMFIs 6.315 0.044 6.375 GetMetaclusters 6.331 0.011 6.361 GetMFIs 6.333 0.004 6.355 GetMetaclusterPercentagesPositive 6.220 0.032 6.269 FlowSOMSubset 6.157 0.035 6.225 GetCounts 6.013 0.015 6.044 GetClusterPercentagesPositive 6.015 0.008 6.044 GetClusters 6.017 0.000 6.034 NewData 5.257 0.008 5.280 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.
FlowSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL FlowSOM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘FlowSOM’ ... ** this is package ‘FlowSOM’ version ‘2.16.0’ ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c som.c -o som.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-devel_2025-02-19/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 | 12.304 | 0.170 | 12.515 | |
AggregateFlowFrames | 0.083 | 0.004 | 0.087 | |
BuildMST | 2.143 | 0.035 | 2.187 | |
BuildSOM | 1.770 | 0.029 | 1.811 | |
CountGroups | 8.827 | 0.125 | 8.999 | |
FMeasure | 0.002 | 0.000 | 0.002 | |
FlowSOM | 16.819 | 0.111 | 16.999 | |
FlowSOMSubset | 6.157 | 0.035 | 6.225 | |
FlowSOMmary | 83.389 | 0.318 | 83.781 | |
GetChannels | 0.033 | 0.000 | 0.033 | |
GetClusterMFIs | 6.315 | 0.044 | 6.375 | |
GetClusterPercentagesPositive | 6.015 | 0.008 | 6.044 | |
GetClusters | 6.017 | 0.000 | 6.034 | |
GetCounts | 6.013 | 0.015 | 6.044 | |
GetFeatures | 7.495 | 0.024 | 7.541 | |
GetFlowJoLabels | 9.841 | 0.072 | 9.942 | |
GetMFIs | 6.333 | 0.004 | 6.355 | |
GetMarkers | 0.033 | 0.000 | 0.033 | |
GetMetaclusterCVs | 6.463 | 0.012 | 6.493 | |
GetMetaclusterMFIs | 6.367 | 0.052 | 6.437 | |
GetMetaclusterPercentagesPositive | 6.220 | 0.032 | 6.269 | |
GetMetaclusters | 6.331 | 0.011 | 6.361 | |
GetPercentages | 6.366 | 0.036 | 6.420 | |
GroupStats | 18.046 | 0.039 | 18.140 | |
Initialize_KWSP | 0.006 | 0.000 | 0.006 | |
Initialize_PCA | 0.001 | 0.000 | 0.001 | |
MetaClustering | 4.403 | 0.056 | 4.476 | |
MetaclusterCVs | 6.403 | 0.008 | 6.438 | |
MetaclusterMFIs | 7.014 | 0.044 | 7.079 | |
NClusters | 6.725 | 0.020 | 6.764 | |
NMetaclusters | 7.144 | 0.028 | 7.193 | |
NewData | 5.257 | 0.008 | 5.280 | |
Plot2DScatters | 13.873 | 0.052 | 13.983 | |
PlotCenters | 1.852 | 0.004 | 1.861 | |
PlotClusters2D | 1.737 | 0.000 | 1.742 | |
PlotDimRed | 80.798 | 0.143 | 81.103 | |
PlotFileScatters | 1.713 | 0.012 | 1.734 | |
PlotFlowSOM | 8.580 | 0.060 | 8.663 | |
PlotGroups | 17.013 | 0.016 | 17.074 | |
PlotLabels | 7.607 | 0.004 | 7.632 | |
PlotManualBars | 12.594 | 0.020 | 12.651 | |
PlotMarker | 25.111 | 0.088 | 25.274 | |
PlotNode | 10.271 | 0.036 | 10.329 | |
PlotNumbers | 9.627 | 0.016 | 9.665 | |
PlotOutliers | 43.899 | 0.091 | 44.094 | |
PlotOverview2D | 7.041 | 0.076 | 7.131 | |
PlotPies | 10.012 | 0.028 | 10.060 | |
PlotSD | 3.066 | 0.044 | 3.119 | |
PlotStars | 20.539 | 0.032 | 20.613 | |
PlotVariable | 9.438 | 0.028 | 9.491 | |
Purity | 0.001 | 0.000 | 0.001 | |
QueryMultiple | 13.678 | 0.028 | 13.738 | |
QueryStarPlot | 10.046 | 0.020 | 10.084 | |
ReadInput | 4.710 | 0.048 | 4.766 | |
SaveClustersToFCS | 8.296 | 0.020 | 8.333 | |
TestOutliers | 6.887 | 0.004 | 6.905 | |
UpdateMetaclusters | 23.889 | 0.143 | 24.094 | |
UpdateNodeSize | 8.799 | 0.016 | 8.837 | |
get_channels | 0.028 | 0.004 | 0.032 | |
get_markers | 0.032 | 0.000 | 0.032 | |
metaClustering_consensus | 3.760 | 0.060 | 3.828 | |
plotStarLegend | 0.606 | 0.008 | 0.615 | |
print.FlowSOM | 6.497 | 0.028 | 6.540 | |
query_multiple | 14.025 | 0.032 | 14.091 | |