Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-04-02 19:28 -0400 (Wed, 02 Apr 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
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 742/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FlowSOM 2.14.0 (landing page) Sofie Van Gassen
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 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: 2.14.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FlowSOM_2.14.0.tar.gz |
StartedAt: 2025-03-31 22:15:05 -0400 (Mon, 31 Mar 2025) |
EndedAt: 2025-03-31 22:23:58 -0400 (Mon, 31 Mar 2025) |
EllapsedTime: 532.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FlowSOM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FlowSOM_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’ * using R version 4.4.3 (2025-02-28) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.14.0’ * 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 ... OK * 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 44.906 0.323 45.041 PlotDimRed 42.580 0.181 42.728 PlotOutliers 16.394 0.008 16.402 PlotMarker 15.232 0.032 15.264 UpdateMetaclusters 14.358 0.014 14.373 PlotStars 12.516 0.020 12.535 GroupStats 10.735 0.021 10.757 FlowSOM 10.202 0.076 10.279 PlotGroups 9.496 0.034 9.530 QueryMultiple 8.008 0.005 8.012 Plot2DScatters 7.824 0.029 7.842 query_multiple 7.821 0.009 7.830 AddAnnotation 7.460 0.152 7.613 PlotVariable 6.866 0.008 6.877 PlotManualBars 6.833 0.007 6.841 PlotNumbers 6.524 0.012 6.538 GetFlowJoLabels 6.294 0.146 6.441 QueryStarPlot 6.110 0.012 6.123 PlotNode 6.078 0.005 6.083 PlotFlowSOM 5.569 0.061 5.629 CountGroups 5.516 0.031 5.548 PlotPies 5.471 0.008 5.480 UpdateNodeSize 5.423 0.013 5.437 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.
FlowSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL FlowSOM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘FlowSOM’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c som.c -o som.o gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/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 | 7.460 | 0.152 | 7.613 | |
AggregateFlowFrames | 0.075 | 0.005 | 0.080 | |
BuildMST | 1.248 | 0.006 | 1.254 | |
BuildSOM | 1.019 | 0.015 | 1.033 | |
CountGroups | 5.516 | 0.031 | 5.548 | |
FMeasure | 0.001 | 0.000 | 0.002 | |
FlowSOM | 10.202 | 0.076 | 10.279 | |
FlowSOMSubset | 4.026 | 0.023 | 4.050 | |
FlowSOMmary | 44.906 | 0.323 | 45.041 | |
GetChannels | 0.027 | 0.001 | 0.028 | |
GetClusterMFIs | 3.898 | 0.100 | 3.997 | |
GetClusterPercentagesPositive | 3.580 | 0.036 | 3.616 | |
GetClusters | 3.525 | 0.014 | 3.539 | |
GetCounts | 3.568 | 0.008 | 3.576 | |
GetFeatures | 4.679 | 0.013 | 4.692 | |
GetFlowJoLabels | 6.294 | 0.146 | 6.441 | |
GetMFIs | 3.907 | 0.016 | 3.923 | |
GetMarkers | 0.026 | 0.000 | 0.026 | |
GetMetaclusterCVs | 3.997 | 0.062 | 4.062 | |
GetMetaclusterMFIs | 4.042 | 0.004 | 4.047 | |
GetMetaclusterPercentagesPositive | 4.756 | 0.024 | 4.782 | |
GetMetaclusters | 3.918 | 0.010 | 3.929 | |
GetPercentages | 4.296 | 0.004 | 4.300 | |
GroupStats | 10.735 | 0.021 | 10.757 | |
Initialize_KWSP | 0.003 | 0.000 | 0.003 | |
Initialize_PCA | 0 | 0 | 0 | |
MetaClustering | 2.801 | 0.062 | 2.864 | |
MetaclusterCVs | 4.029 | 0.017 | 4.047 | |
MetaclusterMFIs | 4.508 | 0.013 | 4.521 | |
NClusters | 4.878 | 0.077 | 4.956 | |
NMetaclusters | 4.967 | 0.014 | 4.981 | |
NewData | 4.230 | 0.026 | 4.256 | |
Plot2DScatters | 7.824 | 0.029 | 7.842 | |
PlotCenters | 0.968 | 0.000 | 0.968 | |
PlotClusters2D | 0.988 | 0.001 | 0.989 | |
PlotDimRed | 42.580 | 0.181 | 42.728 | |
PlotFileScatters | 0.697 | 0.021 | 0.718 | |
PlotFlowSOM | 5.569 | 0.061 | 5.629 | |
PlotGroups | 9.496 | 0.034 | 9.530 | |
PlotLabels | 4.570 | 0.010 | 4.579 | |
PlotManualBars | 6.833 | 0.007 | 6.841 | |
PlotMarker | 15.232 | 0.032 | 15.264 | |
PlotNode | 6.078 | 0.005 | 6.083 | |
PlotNumbers | 6.524 | 0.012 | 6.538 | |
PlotOutliers | 16.394 | 0.008 | 16.402 | |
PlotOverview2D | 4.302 | 0.005 | 4.307 | |
PlotPies | 5.471 | 0.008 | 5.480 | |
PlotSD | 1.830 | 0.003 | 1.833 | |
PlotStars | 12.516 | 0.020 | 12.535 | |
PlotVariable | 6.866 | 0.008 | 6.877 | |
Purity | 0.001 | 0.000 | 0.001 | |
QueryMultiple | 8.008 | 0.005 | 8.012 | |
QueryStarPlot | 6.110 | 0.012 | 6.123 | |
ReadInput | 2.800 | 0.034 | 2.834 | |
SaveClustersToFCS | 4.734 | 0.014 | 4.747 | |
TestOutliers | 4.373 | 0.007 | 4.380 | |
UpdateMetaclusters | 14.358 | 0.014 | 14.373 | |
UpdateNodeSize | 5.423 | 0.013 | 5.437 | |
get_channels | 0.026 | 0.000 | 0.027 | |
get_markers | 0.026 | 0.000 | 0.027 | |
metaClustering_consensus | 2.219 | 0.012 | 2.231 | |
plotStarLegend | 0.364 | 0.002 | 0.366 | |
print.FlowSOM | 4.172 | 0.012 | 4.184 | |
query_multiple | 7.821 | 0.009 | 7.830 | |