Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-03 12:07 -0400 (Fri, 03 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" | 4845 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4632 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4577 |
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: FlowSOM |
Version: 2.17.0 |
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_2.17.0.tar.gz |
StartedAt: 2025-10-03 07:13:18 -0000 (Fri, 03 Oct 2025) |
EndedAt: 2025-10-03 07:25:03 -0000 (Fri, 03 Oct 2025) |
EllapsedTime: 705.0 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_2.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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) * 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: ‘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 73.732 0.279 74.139 PlotDimRed 71.179 0.175 71.503 PlotOutliers 42.701 0.124 42.952 PlotMarker 23.330 0.099 23.492 UpdateMetaclusters 22.353 0.134 22.546 PlotStars 18.872 0.032 18.951 GroupStats 16.321 0.107 16.472 FlowSOM 15.617 0.039 15.700 PlotGroups 15.228 0.020 15.296 QueryMultiple 13.363 0.048 13.442 query_multiple 13.079 0.016 13.131 Plot2DScatters 12.706 0.040 12.785 AddAnnotation 11.873 0.088 11.995 PlotManualBars 11.620 0.028 11.677 QueryStarPlot 9.873 0.024 9.922 GetFlowJoLabels 9.180 0.115 9.328 PlotNumbers 9.129 0.032 9.183 PlotNode 9.023 0.028 9.074 PlotPies 8.895 0.071 8.995 UpdateNodeSize 8.699 0.025 8.746 PlotVariable 8.364 0.024 8.409 CountGroups 8.047 0.028 8.094 PlotFlowSOM 7.618 0.088 7.730 GetFeatures 7.192 0.060 7.271 PlotLabels 7.165 0.016 7.199 SaveClustersToFCS 6.930 0.020 6.969 PlotOverview2D 6.386 0.080 6.485 MetaclusterMFIs 6.204 0.028 6.249 TestOutliers 6.202 0.016 6.236 NMetaclusters 6.161 0.044 6.223 NClusters 6.158 0.000 6.177 MetaclusterCVs 6.012 0.012 6.041 GetMFIs 5.903 0.088 6.007 GetMetaclusters 5.669 0.056 5.738 GetMetaclusterCVs 5.548 0.076 5.636 print.FlowSOM 5.568 0.032 5.614 GetPercentages 5.518 0.044 5.574 FlowSOMSubset 5.537 0.024 5.576 GetMetaclusterMFIs 5.480 0.036 5.528 GetMetaclusterPercentagesPositive 5.422 0.036 5.469 GetCounts 5.299 0.072 5.384 GetClusterPercentagesPositive 5.273 0.008 5.293 GetClusterMFIs 5.189 0.088 5.290 GetClusters 5.204 0.012 5.227 * 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-3.22-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-4.5.0/site-library’ * installing *source* package ‘FlowSOM’ ... ** this is package ‘FlowSOM’ version ‘2.17.0’ ** 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-4.5.0/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-4.5.0/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/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 | 11.873 | 0.088 | 11.995 | |
AggregateFlowFrames | 0.078 | 0.004 | 0.082 | |
BuildMST | 2.015 | 0.012 | 2.033 | |
BuildSOM | 1.698 | 0.012 | 1.714 | |
CountGroups | 8.047 | 0.028 | 8.094 | |
FMeasure | 0.002 | 0.000 | 0.002 | |
FlowSOM | 15.617 | 0.039 | 15.700 | |
FlowSOMSubset | 5.537 | 0.024 | 5.576 | |
FlowSOMmary | 73.732 | 0.279 | 74.139 | |
GetChannels | 0.032 | 0.000 | 0.031 | |
GetClusterMFIs | 5.189 | 0.088 | 5.290 | |
GetClusterPercentagesPositive | 5.273 | 0.008 | 5.293 | |
GetClusters | 5.204 | 0.012 | 5.227 | |
GetCounts | 5.299 | 0.072 | 5.384 | |
GetFeatures | 7.192 | 0.060 | 7.271 | |
GetFlowJoLabels | 9.180 | 0.115 | 9.328 | |
GetMFIs | 5.903 | 0.088 | 6.007 | |
GetMarkers | 0.031 | 0.000 | 0.030 | |
GetMetaclusterCVs | 5.548 | 0.076 | 5.636 | |
GetMetaclusterMFIs | 5.480 | 0.036 | 5.528 | |
GetMetaclusterPercentagesPositive | 5.422 | 0.036 | 5.469 | |
GetMetaclusters | 5.669 | 0.056 | 5.738 | |
GetPercentages | 5.518 | 0.044 | 5.574 | |
GroupStats | 16.321 | 0.107 | 16.472 | |
Initialize_KWSP | 0.006 | 0.000 | 0.006 | |
Initialize_PCA | 0.001 | 0.000 | 0.001 | |
MetaClustering | 4.159 | 0.044 | 4.216 | |
MetaclusterCVs | 6.012 | 0.012 | 6.041 | |
MetaclusterMFIs | 6.204 | 0.028 | 6.249 | |
NClusters | 6.158 | 0.000 | 6.177 | |
NMetaclusters | 6.161 | 0.044 | 6.223 | |
NewData | 4.555 | 0.048 | 4.616 | |
Plot2DScatters | 12.706 | 0.040 | 12.785 | |
PlotCenters | 1.770 | 0.024 | 1.799 | |
PlotClusters2D | 1.623 | 0.000 | 1.628 | |
PlotDimRed | 71.179 | 0.175 | 71.503 | |
PlotFileScatters | 1.571 | 0.020 | 1.596 | |
PlotFlowSOM | 7.618 | 0.088 | 7.730 | |
PlotGroups | 15.228 | 0.020 | 15.296 | |
PlotLabels | 7.165 | 0.016 | 7.199 | |
PlotManualBars | 11.620 | 0.028 | 11.677 | |
PlotMarker | 23.330 | 0.099 | 23.492 | |
PlotNode | 9.023 | 0.028 | 9.074 | |
PlotNumbers | 9.129 | 0.032 | 9.183 | |
PlotOutliers | 42.701 | 0.124 | 42.952 | |
PlotOverview2D | 6.386 | 0.080 | 6.485 | |
PlotPies | 8.895 | 0.071 | 8.995 | |
PlotSD | 2.859 | 0.016 | 2.882 | |
PlotStars | 18.872 | 0.032 | 18.951 | |
PlotVariable | 8.364 | 0.024 | 8.409 | |
Purity | 0.001 | 0.000 | 0.001 | |
QueryMultiple | 13.363 | 0.048 | 13.442 | |
QueryStarPlot | 9.873 | 0.024 | 9.922 | |
ReadInput | 4.296 | 0.064 | 4.371 | |
SaveClustersToFCS | 6.930 | 0.020 | 6.969 | |
TestOutliers | 6.202 | 0.016 | 6.236 | |
UpdateMetaclusters | 22.353 | 0.134 | 22.546 | |
UpdateNodeSize | 8.699 | 0.025 | 8.746 | |
get_channels | 0.028 | 0.004 | 0.032 | |
get_markers | 0.032 | 0.000 | 0.031 | |
metaClustering_consensus | 3.350 | 0.056 | 3.413 | |
plotStarLegend | 0.600 | 0.000 | 0.601 | |
print.FlowSOM | 5.568 | 0.032 | 5.614 | |
query_multiple | 13.079 | 0.016 | 13.131 | |