Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:04 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 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 758/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FlowSOM 2.17.0 (landing page) Sofie Van Gassen
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | 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. |
Package: FlowSOM |
Version: 2.17.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.17.0.tar.gz |
StartedAt: 2025-10-10 21:55:24 -0400 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 22:07:42 -0400 (Fri, 10 Oct 2025) |
EllapsedTime: 738.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FlowSOM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.17.0’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.1.sdk’ * 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 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed FlowSOMmary 51.482 3.685 59.666 PlotDimRed 45.354 3.075 49.704 PlotOutliers 38.321 1.292 40.485 PlotMarker 21.692 1.441 24.033 UpdateMetaclusters 18.589 1.494 20.814 PlotStars 16.073 1.459 18.990 GroupStats 14.327 1.443 16.843 PlotGroups 13.829 1.156 15.237 FlowSOM 12.149 1.480 14.468 Plot2DScatters 11.417 2.057 15.448 QueryMultiple 10.468 0.855 13.833 AddAnnotation 9.727 0.766 10.660 query_multiple 9.700 0.689 12.990 PlotManualBars 9.016 1.054 10.182 PlotNode 8.032 1.340 11.695 GetFlowJoLabels 7.566 0.800 9.203 PlotPies 7.240 1.111 9.567 PlotNumbers 7.293 1.004 8.668 PlotVariable 7.011 0.949 9.407 PlotFlowSOM 6.870 0.864 7.930 UpdateNodeSize 6.904 0.357 7.761 SaveClustersToFCS 5.812 1.325 8.638 CountGroups 6.311 0.787 7.281 PlotOverview2D 5.890 1.174 10.019 QueryStarPlot 6.470 0.591 9.499 PlotLabels 5.809 0.804 6.722 MetaclusterMFIs 4.824 1.439 9.251 NClusters 4.954 1.251 8.055 GetFeatures 5.582 0.590 6.369 NMetaclusters 4.902 1.250 8.226 GetMetaclusters 4.722 1.199 7.296 TestOutliers 5.050 0.834 6.052 MetaclusterCVs 4.413 1.349 7.740 GetMFIs 4.536 1.121 7.524 print.FlowSOM 4.437 1.171 5.778 GetPercentages 4.650 0.909 5.849 GetMetaclusterPercentagesPositive 4.173 1.308 7.987 GetMetaclusterMFIs 4.161 1.243 8.270 GetMetaclusterCVs 4.509 0.812 5.751 GetClusterMFIs 4.354 0.813 6.073 GetClusterPercentagesPositive 4.335 0.718 5.855 GetClusters 4.276 0.739 5.456 FlowSOMSubset 4.225 0.617 5.713 GetCounts 3.939 0.819 5.727 NewData 3.596 0.868 5.796 ReadInput 3.113 0.709 5.215 * 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 ‘/Users/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.
FlowSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘FlowSOM’ ... ** this is package ‘FlowSOM’ version ‘2.17.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c som.c -o som.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 | 9.727 | 0.766 | 10.660 | |
AggregateFlowFrames | 0.104 | 0.010 | 0.117 | |
BuildMST | 1.556 | 0.135 | 1.715 | |
BuildSOM | 1.329 | 0.115 | 1.479 | |
CountGroups | 6.311 | 0.787 | 7.281 | |
FMeasure | 0.002 | 0.000 | 0.002 | |
FlowSOM | 12.149 | 1.480 | 14.468 | |
FlowSOMSubset | 4.225 | 0.617 | 5.713 | |
FlowSOMmary | 51.482 | 3.685 | 59.666 | |
GetChannels | 0.043 | 0.011 | 0.077 | |
GetClusterMFIs | 4.354 | 0.813 | 6.073 | |
GetClusterPercentagesPositive | 4.335 | 0.718 | 5.855 | |
GetClusters | 4.276 | 0.739 | 5.456 | |
GetCounts | 3.939 | 0.819 | 5.727 | |
GetFeatures | 5.582 | 0.590 | 6.369 | |
GetFlowJoLabels | 7.566 | 0.800 | 9.203 | |
GetMFIs | 4.536 | 1.121 | 7.524 | |
GetMarkers | 0.060 | 0.050 | 0.115 | |
GetMetaclusterCVs | 4.509 | 0.812 | 5.751 | |
GetMetaclusterMFIs | 4.161 | 1.243 | 8.270 | |
GetMetaclusterPercentagesPositive | 4.173 | 1.308 | 7.987 | |
GetMetaclusters | 4.722 | 1.199 | 7.296 | |
GetPercentages | 4.650 | 0.909 | 5.849 | |
GroupStats | 14.327 | 1.443 | 16.843 | |
Initialize_KWSP | 0.004 | 0.001 | 0.005 | |
Initialize_PCA | 0.001 | 0.000 | 0.001 | |
MetaClustering | 3.186 | 0.879 | 4.422 | |
MetaclusterCVs | 4.413 | 1.349 | 7.740 | |
MetaclusterMFIs | 4.824 | 1.439 | 9.251 | |
NClusters | 4.954 | 1.251 | 8.055 | |
NMetaclusters | 4.902 | 1.250 | 8.226 | |
NewData | 3.596 | 0.868 | 5.796 | |
Plot2DScatters | 11.417 | 2.057 | 15.448 | |
PlotCenters | 1.495 | 0.233 | 1.903 | |
PlotClusters2D | 1.380 | 0.278 | 1.758 | |
PlotDimRed | 45.354 | 3.075 | 49.704 | |
PlotFileScatters | 2.013 | 0.123 | 2.174 | |
PlotFlowSOM | 6.870 | 0.864 | 7.930 | |
PlotGroups | 13.829 | 1.156 | 15.237 | |
PlotLabels | 5.809 | 0.804 | 6.722 | |
PlotManualBars | 9.016 | 1.054 | 10.182 | |
PlotMarker | 21.692 | 1.441 | 24.033 | |
PlotNode | 8.032 | 1.340 | 11.695 | |
PlotNumbers | 7.293 | 1.004 | 8.668 | |
PlotOutliers | 38.321 | 1.292 | 40.485 | |
PlotOverview2D | 5.890 | 1.174 | 10.019 | |
PlotPies | 7.240 | 1.111 | 9.567 | |
PlotSD | 2.246 | 0.151 | 2.425 | |
PlotStars | 16.073 | 1.459 | 18.990 | |
PlotVariable | 7.011 | 0.949 | 9.407 | |
Purity | 0.000 | 0.000 | 0.012 | |
QueryMultiple | 10.468 | 0.855 | 13.833 | |
QueryStarPlot | 6.470 | 0.591 | 9.499 | |
ReadInput | 3.113 | 0.709 | 5.215 | |
SaveClustersToFCS | 5.812 | 1.325 | 8.638 | |
TestOutliers | 5.050 | 0.834 | 6.052 | |
UpdateMetaclusters | 18.589 | 1.494 | 20.814 | |
UpdateNodeSize | 6.904 | 0.357 | 7.761 | |
get_channels | 0.044 | 0.004 | 0.049 | |
get_markers | 0.046 | 0.003 | 0.051 | |
metaClustering_consensus | 2.349 | 0.492 | 2.885 | |
plotStarLegend | 0.518 | 0.007 | 0.529 | |
print.FlowSOM | 4.437 | 1.171 | 5.778 | |
query_multiple | 9.700 | 0.689 | 12.990 | |