Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:47 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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: 2025-08-01 09:24:21 -0000 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 09:36:05 -0000 (Fri, 01 Aug 2025) |
EllapsedTime: 704.4 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 PlotDimRed 78.957 0.160 79.238 FlowSOMmary 73.436 0.307 73.810 PlotOutliers 24.814 0.096 24.974 UpdateMetaclusters 21.991 0.072 22.124 PlotMarker 21.734 0.052 21.841 PlotStars 18.891 0.040 18.973 GroupStats 16.547 0.079 16.670 FlowSOM 16.262 0.132 16.431 PlotGroups 15.456 0.004 15.500 AddAnnotation 11.835 0.208 12.075 QueryMultiple 11.756 0.020 11.806 query_multiple 11.744 0.016 11.791 Plot2DScatters 10.782 0.020 10.830 PlotManualBars 10.482 0.012 10.519 GetFlowJoLabels 9.774 0.056 9.857 PlotNode 9.575 0.020 9.621 CountGroups 9.020 0.072 9.113 PlotVariable 8.827 0.047 8.898 QueryStarPlot 8.848 0.008 8.877 PlotNumbers 8.795 0.012 8.830 PlotPies 8.479 0.016 8.516 PlotFlowSOM 7.776 0.048 7.841 UpdateNodeSize 7.744 0.004 7.769 SaveClustersToFCS 7.651 0.004 7.675 NClusters 7.421 0.008 7.446 GetFeatures 7.325 0.044 7.388 PlotLabels 7.185 0.040 7.240 NMetaclusters 7.020 0.016 7.051 TestOutliers 6.726 0.044 6.791 MetaclusterMFIs 6.562 0.016 6.596 GetMetaclusterPercentagesPositive 6.475 0.020 6.508 PlotOverview2D 6.365 0.036 6.416 GetMetaclusterCVs 6.309 0.028 6.351 MetaclusterCVs 6.210 0.032 6.256 print.FlowSOM 6.221 0.008 6.245 GetMFIs 6.177 0.012 6.203 FlowSOMSubset 6.154 0.008 6.176 GetMetaclusters 6.122 0.032 6.169 GetPercentages 6.119 0.004 6.137 GetMetaclusterMFIs 6.110 0.008 6.133 GetCounts 5.739 0.008 5.761 GetClusterMFIs 5.668 0.064 5.747 GetClusterPercentagesPositive 5.716 0.012 5.744 GetClusters 5.688 0.012 5.715 NewData 5.138 0.044 5.194 ReadInput 5.100 0.024 5.137 * 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 | 11.835 | 0.208 | 12.075 | |
AggregateFlowFrames | 0.087 | 0.012 | 0.099 | |
BuildMST | 2.066 | 0.015 | 2.088 | |
BuildSOM | 1.808 | 0.020 | 1.832 | |
CountGroups | 9.020 | 0.072 | 9.113 | |
FMeasure | 0.002 | 0.000 | 0.002 | |
FlowSOM | 16.262 | 0.132 | 16.431 | |
FlowSOMSubset | 6.154 | 0.008 | 6.176 | |
FlowSOMmary | 73.436 | 0.307 | 73.810 | |
GetChannels | 0.031 | 0.000 | 0.031 | |
GetClusterMFIs | 5.668 | 0.064 | 5.747 | |
GetClusterPercentagesPositive | 5.716 | 0.012 | 5.744 | |
GetClusters | 5.688 | 0.012 | 5.715 | |
GetCounts | 5.739 | 0.008 | 5.761 | |
GetFeatures | 7.325 | 0.044 | 7.388 | |
GetFlowJoLabels | 9.774 | 0.056 | 9.857 | |
GetMFIs | 6.177 | 0.012 | 6.203 | |
GetMarkers | 0.034 | 0.000 | 0.034 | |
GetMetaclusterCVs | 6.309 | 0.028 | 6.351 | |
GetMetaclusterMFIs | 6.110 | 0.008 | 6.133 | |
GetMetaclusterPercentagesPositive | 6.475 | 0.020 | 6.508 | |
GetMetaclusters | 6.122 | 0.032 | 6.169 | |
GetPercentages | 6.119 | 0.004 | 6.137 | |
GroupStats | 16.547 | 0.079 | 16.670 | |
Initialize_KWSP | 0.006 | 0.000 | 0.007 | |
Initialize_PCA | 0.001 | 0.000 | 0.001 | |
MetaClustering | 4.517 | 0.024 | 4.551 | |
MetaclusterCVs | 6.210 | 0.032 | 6.256 | |
MetaclusterMFIs | 6.562 | 0.016 | 6.596 | |
NClusters | 7.421 | 0.008 | 7.446 | |
NMetaclusters | 7.020 | 0.016 | 7.051 | |
NewData | 5.138 | 0.044 | 5.194 | |
Plot2DScatters | 10.782 | 0.020 | 10.830 | |
PlotCenters | 1.744 | 0.000 | 1.748 | |
PlotClusters2D | 1.745 | 0.000 | 1.749 | |
PlotDimRed | 78.957 | 0.160 | 79.238 | |
PlotFileScatters | 1.062 | 0.039 | 1.106 | |
PlotFlowSOM | 7.776 | 0.048 | 7.841 | |
PlotGroups | 15.456 | 0.004 | 15.500 | |
PlotLabels | 7.185 | 0.040 | 7.240 | |
PlotManualBars | 10.482 | 0.012 | 10.519 | |
PlotMarker | 21.734 | 0.052 | 21.841 | |
PlotNode | 9.575 | 0.020 | 9.621 | |
PlotNumbers | 8.795 | 0.012 | 8.830 | |
PlotOutliers | 24.814 | 0.096 | 24.974 | |
PlotOverview2D | 6.365 | 0.036 | 6.416 | |
PlotPies | 8.479 | 0.016 | 8.516 | |
PlotSD | 2.889 | 0.000 | 2.896 | |
PlotStars | 18.891 | 0.040 | 18.973 | |
PlotVariable | 8.827 | 0.047 | 8.898 | |
Purity | 0.001 | 0.000 | 0.001 | |
QueryMultiple | 11.756 | 0.020 | 11.806 | |
QueryStarPlot | 8.848 | 0.008 | 8.877 | |
ReadInput | 5.100 | 0.024 | 5.137 | |
SaveClustersToFCS | 7.651 | 0.004 | 7.675 | |
TestOutliers | 6.726 | 0.044 | 6.791 | |
UpdateMetaclusters | 21.991 | 0.072 | 22.124 | |
UpdateNodeSize | 7.744 | 0.004 | 7.769 | |
get_channels | 0.048 | 0.000 | 0.048 | |
get_markers | 0.033 | 0.000 | 0.034 | |
metaClustering_consensus | 3.761 | 0.012 | 3.783 | |
plotStarLegend | 0.487 | 0.004 | 0.491 | |
print.FlowSOM | 6.221 | 0.008 | 6.245 | |
query_multiple | 11.744 | 0.016 | 11.791 | |