Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:40:32 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 750/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FlowSOM 2.12.0 (landing page) Sofie Van Gassen
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 2.12.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings FlowSOM_2.12.0.tar.gz |
StartedAt: 2024-05-04 07:36:13 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 07:48:15 -0000 (Sat, 04 May 2024) |
EllapsedTime: 722.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FlowSOM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings FlowSOM_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.12.0’ * 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 (GCC) 10.3.1’ * 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 PlotDimRed 87.433 0.140 87.750 FlowSOMmary 79.346 0.387 79.750 PlotOutliers 24.855 0.104 25.014 PlotMarker 23.542 0.108 23.701 UpdateMetaclusters 21.743 0.072 21.861 PlotStars 18.928 0.048 19.015 GroupStats 17.942 0.036 18.017 FlowSOM 16.856 0.108 16.999 PlotGroups 15.933 0.040 16.008 AddAnnotation 12.350 0.244 12.623 query_multiple 12.043 0.060 12.129 QueryMultiple 11.933 0.048 12.005 Plot2DScatters 11.411 0.044 11.472 PlotManualBars 10.808 0.032 10.863 GetFlowJoLabels 10.362 0.060 10.448 PlotNode 9.788 0.028 9.836 CountGroups 9.363 0.118 9.501 QueryStarPlot 9.424 0.032 9.476 PlotNumbers 9.329 0.020 9.369 PlotVariable 8.860 0.035 8.913 PlotPies 8.868 0.008 8.896 PlotFlowSOM 8.173 0.047 8.237 UpdateNodeSize 7.969 0.028 8.012 SaveClustersToFCS 7.607 0.056 7.679 GetFeatures 7.504 0.004 7.524 PlotLabels 7.220 0.016 7.250 NMetaclusters 7.179 0.048 7.244 NClusters 7.144 0.027 7.187 MetaclusterMFIs 7.101 0.060 7.175 TestOutliers 6.760 0.008 6.782 GetPercentages 6.728 0.016 6.759 PlotOverview2D 6.654 0.012 6.681 MetaclusterCVs 6.559 0.028 6.599 GetMetaclusterCVs 6.503 0.024 6.541 GetMetaclusters 6.341 0.064 6.419 GetMFIs 6.312 0.076 6.403 GetClusters 6.344 0.035 6.394 GetMetaclusterMFIs 6.367 0.008 6.388 FlowSOMSubset 6.249 0.076 6.338 GetMetaclusterPercentagesPositive 6.289 0.000 6.300 GetClusterPercentagesPositive 6.228 0.040 6.281 print.FlowSOM 6.095 0.016 6.123 GetClusterMFIs 6.001 0.068 6.082 GetCounts 5.985 0.012 6.014 NewData 5.218 0.012 5.240 ReadInput 5.191 0.032 5.233 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.
FlowSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL FlowSOM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘FlowSOM’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c som.c -o som.o gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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 | 12.350 | 0.244 | 12.623 | |
AggregateFlowFrames | 0.096 | 0.011 | 0.108 | |
BuildMST | 2.225 | 0.025 | 2.253 | |
BuildSOM | 1.884 | 0.011 | 1.900 | |
CountGroups | 9.363 | 0.118 | 9.501 | |
FMeasure | 0.002 | 0.000 | 0.002 | |
FlowSOM | 16.856 | 0.108 | 16.999 | |
FlowSOMSubset | 6.249 | 0.076 | 6.338 | |
FlowSOMmary | 79.346 | 0.387 | 79.750 | |
GetChannels | 0.033 | 0.004 | 0.038 | |
GetClusterMFIs | 6.001 | 0.068 | 6.082 | |
GetClusterPercentagesPositive | 6.228 | 0.040 | 6.281 | |
GetClusters | 6.344 | 0.035 | 6.394 | |
GetCounts | 5.985 | 0.012 | 6.014 | |
GetFeatures | 7.504 | 0.004 | 7.524 | |
GetFlowJoLabels | 10.362 | 0.060 | 10.448 | |
GetMFIs | 6.312 | 0.076 | 6.403 | |
GetMarkers | 0.031 | 0.008 | 0.039 | |
GetMetaclusterCVs | 6.503 | 0.024 | 6.541 | |
GetMetaclusterMFIs | 6.367 | 0.008 | 6.388 | |
GetMetaclusterPercentagesPositive | 6.289 | 0.000 | 6.300 | |
GetMetaclusters | 6.341 | 0.064 | 6.419 | |
GetPercentages | 6.728 | 0.016 | 6.759 | |
GroupStats | 17.942 | 0.036 | 18.017 | |
Initialize_KWSP | 0.006 | 0.000 | 0.006 | |
Initialize_PCA | 0.001 | 0.000 | 0.001 | |
MetaClustering | 4.720 | 0.016 | 4.745 | |
MetaclusterCVs | 6.559 | 0.028 | 6.599 | |
MetaclusterMFIs | 7.101 | 0.060 | 7.175 | |
NClusters | 7.144 | 0.027 | 7.187 | |
NMetaclusters | 7.179 | 0.048 | 7.244 | |
NewData | 5.218 | 0.012 | 5.240 | |
Plot2DScatters | 11.411 | 0.044 | 11.472 | |
PlotCenters | 1.895 | 0.020 | 1.922 | |
PlotClusters2D | 1.865 | 0.004 | 1.879 | |
PlotDimRed | 87.433 | 0.140 | 87.750 | |
PlotFileScatters | 1.462 | 0.076 | 1.541 | |
PlotFlowSOM | 8.173 | 0.047 | 8.237 | |
PlotGroups | 15.933 | 0.040 | 16.008 | |
PlotLabels | 7.220 | 0.016 | 7.250 | |
PlotManualBars | 10.808 | 0.032 | 10.863 | |
PlotMarker | 23.542 | 0.108 | 23.701 | |
PlotNode | 9.788 | 0.028 | 9.836 | |
PlotNumbers | 9.329 | 0.020 | 9.369 | |
PlotOutliers | 24.855 | 0.104 | 25.014 | |
PlotOverview2D | 6.654 | 0.012 | 6.681 | |
PlotPies | 8.868 | 0.008 | 8.896 | |
PlotSD | 3.554 | 0.040 | 3.602 | |
PlotStars | 18.928 | 0.048 | 19.015 | |
PlotVariable | 8.860 | 0.035 | 8.913 | |
Purity | 0.001 | 0.000 | 0.001 | |
QueryMultiple | 11.933 | 0.048 | 12.005 | |
QueryStarPlot | 9.424 | 0.032 | 9.476 | |
ReadInput | 5.191 | 0.032 | 5.233 | |
SaveClustersToFCS | 7.607 | 0.056 | 7.679 | |
TestOutliers | 6.760 | 0.008 | 6.782 | |
UpdateMetaclusters | 21.743 | 0.072 | 21.861 | |
UpdateNodeSize | 7.969 | 0.028 | 8.012 | |
get_channels | 0.034 | 0.000 | 0.034 | |
get_markers | 0.035 | 0.000 | 0.035 | |
metaClustering_consensus | 4.080 | 0.032 | 4.121 | |
plotStarLegend | 0.451 | 0.004 | 0.457 | |
print.FlowSOM | 6.095 | 0.016 | 6.123 | |
query_multiple | 12.043 | 0.060 | 12.129 | |