Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-30 12:05 -0400 (Tue, 30 Sep 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" | 4843 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4575 |
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 757/2337 | 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: 2025-09-29 19:28:19 -0400 (Mon, 29 Sep 2025) |
EndedAt: 2025-09-29 19:31:59 -0400 (Mon, 29 Sep 2025) |
EllapsedTime: 220.6 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: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * 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 15.0.0 (clang-1500.1.0.2.5)’ * 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 19.327 1.087 20.540 PlotDimRed 16.842 1.743 19.043 PlotOutliers 9.636 0.386 10.167 PlotMarker 6.758 0.647 7.690 UpdateMetaclusters 5.869 0.570 6.509 PlotStars 5.077 0.535 5.673 * 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-arm64/Resources/library’ * installing *source* package ‘FlowSOM’ ... ** this is package ‘FlowSOM’ version ‘2.17.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c som.c -o som.o clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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 | 3.124 | 0.209 | 3.498 | |
AggregateFlowFrames | 0.036 | 0.004 | 0.040 | |
BuildMST | 0.533 | 0.048 | 0.591 | |
BuildSOM | 0.394 | 0.043 | 0.447 | |
CountGroups | 2.430 | 0.245 | 2.721 | |
FMeasure | 0 | 0 | 0 | |
FlowSOM | 4.527 | 0.362 | 4.953 | |
FlowSOMSubset | 1.654 | 0.169 | 1.865 | |
FlowSOMmary | 19.327 | 1.087 | 20.540 | |
GetChannels | 0.013 | 0.001 | 0.017 | |
GetClusterMFIs | 1.666 | 0.265 | 2.001 | |
GetClusterPercentagesPositive | 1.649 | 0.223 | 1.904 | |
GetClusters | 1.634 | 0.257 | 1.924 | |
GetCounts | 1.676 | 0.275 | 1.978 | |
GetFeatures | 2.128 | 0.199 | 2.385 | |
GetFlowJoLabels | 2.792 | 0.293 | 3.107 | |
GetMFIs | 1.796 | 0.299 | 2.104 | |
GetMarkers | 0.013 | 0.002 | 0.016 | |
GetMetaclusterCVs | 1.749 | 0.298 | 2.090 | |
GetMetaclusterMFIs | 1.743 | 0.279 | 2.083 | |
GetMetaclusterPercentagesPositive | 1.977 | 0.324 | 2.378 | |
GetMetaclusters | 1.744 | 0.279 | 2.058 | |
GetPercentages | 1.791 | 0.313 | 2.154 | |
GroupStats | 4.419 | 0.415 | 4.919 | |
Initialize_KWSP | 0.001 | 0.000 | 0.001 | |
Initialize_PCA | 0.000 | 0.000 | 0.001 | |
MetaClustering | 1.084 | 0.365 | 1.478 | |
MetaclusterCVs | 1.766 | 0.297 | 2.083 | |
MetaclusterMFIs | 1.922 | 0.369 | 2.298 | |
NClusters | 1.864 | 0.351 | 2.228 | |
NMetaclusters | 1.933 | 0.377 | 2.359 | |
NewData | 1.578 | 0.247 | 1.858 | |
Plot2DScatters | 3.612 | 0.404 | 4.092 | |
PlotCenters | 0.426 | 0.071 | 0.512 | |
PlotClusters2D | 0.403 | 0.064 | 0.484 | |
PlotDimRed | 16.842 | 1.743 | 19.043 | |
PlotFileScatters | 0.361 | 0.011 | 0.376 | |
PlotFlowSOM | 2.202 | 0.407 | 2.667 | |
PlotGroups | 4.182 | 0.595 | 4.900 | |
PlotLabels | 2.437 | 0.352 | 2.808 | |
PlotManualBars | 3.309 | 0.458 | 3.919 | |
PlotMarker | 6.758 | 0.647 | 7.690 | |
PlotNode | 2.567 | 0.305 | 2.890 | |
PlotNumbers | 2.491 | 0.361 | 2.862 | |
PlotOutliers | 9.636 | 0.386 | 10.167 | |
PlotOverview2D | 2.143 | 0.317 | 2.489 | |
PlotPies | 2.689 | 0.361 | 3.112 | |
PlotSD | 0.758 | 0.052 | 0.819 | |
PlotStars | 5.077 | 0.535 | 5.673 | |
PlotVariable | 2.563 | 0.337 | 2.946 | |
Purity | 0.000 | 0.000 | 0.001 | |
QueryMultiple | 3.507 | 0.241 | 3.787 | |
QueryStarPlot | 2.640 | 0.211 | 2.868 | |
ReadInput | 1.259 | 0.317 | 1.584 | |
SaveClustersToFCS | 2.055 | 0.357 | 2.416 | |
TestOutliers | 1.874 | 0.294 | 2.199 | |
UpdateMetaclusters | 5.869 | 0.570 | 6.509 | |
UpdateNodeSize | 2.024 | 0.092 | 2.214 | |
get_channels | 0.013 | 0.002 | 0.015 | |
get_markers | 0.014 | 0.002 | 0.017 | |
metaClustering_consensus | 0.958 | 0.251 | 1.248 | |
plotStarLegend | 0.180 | 0.007 | 0.190 | |
print.FlowSOM | 1.859 | 0.357 | 2.300 | |
query_multiple | 3.650 | 0.252 | 4.030 | |