Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-23 12:07 -0400 (Tue, 23 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" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 756/2334 | 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: 2025-09-23 07:22:07 -0000 (Tue, 23 Sep 2025) |
EndedAt: 2025-09-23 07:34:07 -0000 (Tue, 23 Sep 2025) |
EllapsedTime: 720.0 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 PlotDimRed 75.258 0.220 75.646 FlowSOMmary 74.340 0.354 74.786 PlotOutliers 42.957 0.096 43.179 PlotMarker 23.876 0.119 24.069 UpdateMetaclusters 22.667 0.044 22.769 PlotStars 19.328 0.044 19.420 GroupStats 17.191 0.602 17.841 PlotGroups 15.577 0.024 15.647 FlowSOM 15.491 0.032 15.556 Plot2DScatters 13.203 0.143 13.386 QueryMultiple 13.022 0.048 13.097 query_multiple 13.023 0.000 13.055 AddAnnotation 11.620 0.132 11.779 PlotManualBars 11.572 0.004 11.613 QueryStarPlot 9.701 0.024 9.745 PlotNode 9.597 0.008 9.632 PlotNumbers 9.375 0.044 9.444 GetFlowJoLabels 9.263 0.147 9.433 PlotPies 8.871 0.028 8.925 UpdateNodeSize 8.572 0.024 8.616 PlotVariable 8.472 0.051 8.540 CountGroups 8.221 0.052 8.290 PlotFlowSOM 7.924 0.052 7.999 GetFeatures 6.996 0.084 7.094 SaveClustersToFCS 7.052 0.012 7.080 PlotLabels 6.978 0.071 7.070 GetPercentages 6.483 0.403 6.906 PlotOverview2D 6.497 0.028 6.543 NClusters 6.445 0.079 6.545 NMetaclusters 6.432 0.068 6.519 MetaclusterMFIs 6.396 0.036 6.450 TestOutliers 6.223 0.007 6.244 GetMFIs 5.766 0.100 5.881 GetMetaclusterCVs 5.787 0.076 5.874 GetMetaclusters 5.785 0.063 5.864 MetaclusterCVs 5.740 0.100 5.855 GetClusterMFIs 5.542 0.220 5.774 GetMetaclusterPercentagesPositive 5.653 0.056 5.723 GetMetaclusterMFIs 5.617 0.076 5.702 print.FlowSOM 5.626 0.016 5.655 GetClusterPercentagesPositive 5.470 0.131 5.614 GetCounts 5.488 0.060 5.560 GetClusters 5.407 0.088 5.511 FlowSOMSubset 5.248 0.024 5.284 * 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 | 11.620 | 0.132 | 11.779 | |
AggregateFlowFrames | 0.081 | 0.004 | 0.086 | |
BuildMST | 2.014 | 0.004 | 2.021 | |
BuildSOM | 1.675 | 0.012 | 1.691 | |
CountGroups | 8.221 | 0.052 | 8.290 | |
FMeasure | 0.002 | 0.000 | 0.002 | |
FlowSOM | 15.491 | 0.032 | 15.556 | |
FlowSOMSubset | 5.248 | 0.024 | 5.284 | |
FlowSOMmary | 74.340 | 0.354 | 74.786 | |
GetChannels | 0.035 | 0.000 | 0.035 | |
GetClusterMFIs | 5.542 | 0.220 | 5.774 | |
GetClusterPercentagesPositive | 5.470 | 0.131 | 5.614 | |
GetClusters | 5.407 | 0.088 | 5.511 | |
GetCounts | 5.488 | 0.060 | 5.560 | |
GetFeatures | 6.996 | 0.084 | 7.094 | |
GetFlowJoLabels | 9.263 | 0.147 | 9.433 | |
GetMFIs | 5.766 | 0.100 | 5.881 | |
GetMarkers | 0.035 | 0.000 | 0.035 | |
GetMetaclusterCVs | 5.787 | 0.076 | 5.874 | |
GetMetaclusterMFIs | 5.617 | 0.076 | 5.702 | |
GetMetaclusterPercentagesPositive | 5.653 | 0.056 | 5.723 | |
GetMetaclusters | 5.785 | 0.063 | 5.864 | |
GetPercentages | 6.483 | 0.403 | 6.906 | |
GroupStats | 17.191 | 0.602 | 17.841 | |
Initialize_KWSP | 0.006 | 0.000 | 0.006 | |
Initialize_PCA | 0.001 | 0.000 | 0.001 | |
MetaClustering | 4.201 | 0.096 | 4.309 | |
MetaclusterCVs | 5.740 | 0.100 | 5.855 | |
MetaclusterMFIs | 6.396 | 0.036 | 6.450 | |
NClusters | 6.445 | 0.079 | 6.545 | |
NMetaclusters | 6.432 | 0.068 | 6.519 | |
NewData | 4.655 | 0.060 | 4.728 | |
Plot2DScatters | 13.203 | 0.143 | 13.386 | |
PlotCenters | 1.763 | 0.024 | 1.792 | |
PlotClusters2D | 1.643 | 0.004 | 1.651 | |
PlotDimRed | 75.258 | 0.220 | 75.646 | |
PlotFileScatters | 1.768 | 0.012 | 1.786 | |
PlotFlowSOM | 7.924 | 0.052 | 7.999 | |
PlotGroups | 15.577 | 0.024 | 15.647 | |
PlotLabels | 6.978 | 0.071 | 7.070 | |
PlotManualBars | 11.572 | 0.004 | 11.613 | |
PlotMarker | 23.876 | 0.119 | 24.069 | |
PlotNode | 9.597 | 0.008 | 9.632 | |
PlotNumbers | 9.375 | 0.044 | 9.444 | |
PlotOutliers | 42.957 | 0.096 | 43.179 | |
PlotOverview2D | 6.497 | 0.028 | 6.543 | |
PlotPies | 8.871 | 0.028 | 8.925 | |
PlotSD | 2.880 | 0.020 | 2.908 | |
PlotStars | 19.328 | 0.044 | 19.420 | |
PlotVariable | 8.472 | 0.051 | 8.540 | |
Purity | 0.001 | 0.000 | 0.001 | |
QueryMultiple | 13.022 | 0.048 | 13.097 | |
QueryStarPlot | 9.701 | 0.024 | 9.745 | |
ReadInput | 4.453 | 0.024 | 4.490 | |
SaveClustersToFCS | 7.052 | 0.012 | 7.080 | |
TestOutliers | 6.223 | 0.007 | 6.244 | |
UpdateMetaclusters | 22.667 | 0.044 | 22.769 | |
UpdateNodeSize | 8.572 | 0.024 | 8.616 | |
get_channels | 0.030 | 0.000 | 0.031 | |
get_markers | 0.031 | 0.000 | 0.031 | |
metaClustering_consensus | 3.773 | 0.072 | 3.853 | |
plotStarLegend | 0.632 | 0.000 | 0.633 | |
print.FlowSOM | 5.626 | 0.016 | 5.655 | |
query_multiple | 13.023 | 0.000 | 13.055 | |