Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-06 12:04 -0400 (Mon, 06 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" | 4853 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 758/2341 | 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: 2025-10-05 21:34:43 -0400 (Sun, 05 Oct 2025) |
EndedAt: 2025-10-05 21:45:23 -0400 (Sun, 05 Oct 2025) |
EllapsedTime: 640.0 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 52.832 2.135 55.201 PlotDimRed 44.143 2.632 47.446 PlotOutliers 36.030 0.932 37.341 PlotMarker 22.483 1.299 24.146 UpdateMetaclusters 17.999 1.368 19.602 PlotStars 16.376 1.130 17.730 GroupStats 14.610 1.011 15.790 FlowSOM 13.143 1.107 14.396 PlotGroups 12.633 1.227 14.037 Plot2DScatters 12.327 0.948 13.499 query_multiple 11.025 0.553 11.746 PlotManualBars 10.342 0.887 11.382 QueryMultiple 10.087 0.636 11.380 AddAnnotation 9.791 0.627 10.514 QueryStarPlot 8.518 0.608 9.792 PlotVariable 7.976 0.819 8.900 GetFlowJoLabels 7.942 0.586 8.604 PlotNode 7.669 0.768 8.548 PlotNumbers 7.277 1.092 8.599 PlotPies 7.359 0.853 8.343 CountGroups 6.463 0.670 7.226 UpdateNodeSize 6.681 0.264 6.999 PlotFlowSOM 6.038 0.758 6.919 SaveClustersToFCS 5.601 1.066 7.190 MetaclusterMFIs 5.813 0.845 6.753 NMetaclusters 5.567 0.865 6.546 GetFeatures 5.991 0.401 6.459 PlotLabels 5.630 0.706 6.417 PlotOverview2D 5.522 0.636 6.252 NClusters 5.278 0.784 6.213 MetaclusterCVs 5.335 0.697 6.116 print.FlowSOM 5.076 0.763 5.951 GetMetaclusters 5.053 0.673 5.794 GetMetaclusterMFIs 4.861 0.688 5.661 GetMetaclusterPercentagesPositive 4.776 0.689 5.567 TestOutliers 4.749 0.675 5.496 GetMetaclusterCVs 4.752 0.656 5.471 GetPercentages 4.747 0.602 5.405 GetMFIs 4.624 0.680 5.364 NewData 4.495 0.482 5.044 * 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 | 9.791 | 0.627 | 10.514 | |
AggregateFlowFrames | 0.099 | 0.006 | 0.104 | |
BuildMST | 1.513 | 0.120 | 1.643 | |
BuildSOM | 1.460 | 0.102 | 1.576 | |
CountGroups | 6.463 | 0.670 | 7.226 | |
FMeasure | 0.002 | 0.000 | 0.003 | |
FlowSOM | 13.143 | 1.107 | 14.396 | |
FlowSOMSubset | 4.423 | 0.462 | 4.922 | |
FlowSOMmary | 52.832 | 2.135 | 55.201 | |
GetChannels | 0.042 | 0.003 | 0.045 | |
GetClusterMFIs | 4.363 | 0.449 | 4.876 | |
GetClusterPercentagesPositive | 4.391 | 0.434 | 4.883 | |
GetClusters | 4.359 | 0.472 | 4.877 | |
GetCounts | 4.456 | 0.470 | 4.980 | |
GetFeatures | 5.991 | 0.401 | 6.459 | |
GetFlowJoLabels | 7.942 | 0.586 | 8.604 | |
GetMFIs | 4.624 | 0.680 | 5.364 | |
GetMarkers | 0.043 | 0.002 | 0.045 | |
GetMetaclusterCVs | 4.752 | 0.656 | 5.471 | |
GetMetaclusterMFIs | 4.861 | 0.688 | 5.661 | |
GetMetaclusterPercentagesPositive | 4.776 | 0.689 | 5.567 | |
GetMetaclusters | 5.053 | 0.673 | 5.794 | |
GetPercentages | 4.747 | 0.602 | 5.405 | |
GroupStats | 14.610 | 1.011 | 15.790 | |
Initialize_KWSP | 0.005 | 0.000 | 0.006 | |
Initialize_PCA | 0.001 | 0.000 | 0.001 | |
MetaClustering | 4.028 | 0.635 | 4.725 | |
MetaclusterCVs | 5.335 | 0.697 | 6.116 | |
MetaclusterMFIs | 5.813 | 0.845 | 6.753 | |
NClusters | 5.278 | 0.784 | 6.213 | |
NMetaclusters | 5.567 | 0.865 | 6.546 | |
NewData | 4.495 | 0.482 | 5.044 | |
Plot2DScatters | 12.327 | 0.948 | 13.499 | |
PlotCenters | 1.490 | 0.099 | 1.605 | |
PlotClusters2D | 1.372 | 0.161 | 1.555 | |
PlotDimRed | 44.143 | 2.632 | 47.446 | |
PlotFileScatters | 1.513 | 0.044 | 1.575 | |
PlotFlowSOM | 6.038 | 0.758 | 6.919 | |
PlotGroups | 12.633 | 1.227 | 14.037 | |
PlotLabels | 5.630 | 0.706 | 6.417 | |
PlotManualBars | 10.342 | 0.887 | 11.382 | |
PlotMarker | 22.483 | 1.299 | 24.146 | |
PlotNode | 7.669 | 0.768 | 8.548 | |
PlotNumbers | 7.277 | 1.092 | 8.599 | |
PlotOutliers | 36.030 | 0.932 | 37.341 | |
PlotOverview2D | 5.522 | 0.636 | 6.252 | |
PlotPies | 7.359 | 0.853 | 8.343 | |
PlotSD | 2.506 | 0.313 | 2.954 | |
PlotStars | 16.376 | 1.130 | 17.730 | |
PlotVariable | 7.976 | 0.819 | 8.900 | |
Purity | 0.001 | 0.000 | 0.002 | |
QueryMultiple | 10.087 | 0.636 | 11.380 | |
QueryStarPlot | 8.518 | 0.608 | 9.792 | |
ReadInput | 3.479 | 0.570 | 4.132 | |
SaveClustersToFCS | 5.601 | 1.066 | 7.190 | |
TestOutliers | 4.749 | 0.675 | 5.496 | |
UpdateMetaclusters | 17.999 | 1.368 | 19.602 | |
UpdateNodeSize | 6.681 | 0.264 | 6.999 | |
get_channels | 0.043 | 0.005 | 0.051 | |
get_markers | 0.047 | 0.002 | 0.050 | |
metaClustering_consensus | 2.715 | 0.386 | 3.161 | |
plotStarLegend | 0.534 | 0.005 | 0.544 | |
print.FlowSOM | 5.076 | 0.763 | 5.951 | |
query_multiple | 11.025 | 0.553 | 11.746 | |