Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:40 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the FlowSOM package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 661/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FlowSOM 2.0.0 (landing page) Sofie Van Gassen
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: FlowSOM |
Version: 2.0.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings FlowSOM_2.0.0.tar.gz |
StartedAt: 2021-10-14 09:52:51 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:00:56 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 485.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FlowSOM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings FlowSOM_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/FlowSOM.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.0.0’ * 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 * 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 R 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 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 ... OK * 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 54.146 0.680 54.831 PlotDimRed 42.647 0.032 42.682 PlotMarker 20.789 0.044 20.837 RelabelMetaclusters 19.939 0.028 19.969 GroupStats 14.733 0.031 14.765 ReassignMetaclusters 14.062 0.020 14.083 PlotGroups 13.949 0.032 13.982 FlowSOM 11.823 0.052 11.874 AddAnnotation 8.889 0.140 9.033 query_multiple 8.425 0.008 8.436 QueryMultiple 8.232 0.012 8.245 UpdateNodeSize 7.560 0.012 7.572 PlotStars 7.515 0.012 7.527 PlotNode 7.346 0.020 7.367 PlotFlowSOM 7.108 0.008 7.116 PlotNumbers 6.816 0.004 6.821 QueryStarPlot 6.777 0.004 6.781 PlotManualBars 6.699 0.014 6.713 Plot2DScatters 6.402 0.032 6.434 GetFlowJoLabels 6.307 0.020 6.328 PlotPies 6.192 0.011 6.204 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.13-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.
FlowSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL FlowSOM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘FlowSOM’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c som.c -o som.o gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/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 | 8.889 | 0.140 | 9.033 | |
AggregateFlowFrames | 0.060 | 0.012 | 0.072 | |
BuildMST | 0.926 | 0.000 | 0.925 | |
BuildSOM | 1.196 | 0.012 | 1.208 | |
CountGroups | 4.923 | 0.060 | 4.983 | |
FMeasure | 0.002 | 0.000 | 0.002 | |
FlowSOM | 11.823 | 0.052 | 11.874 | |
FlowSOMSubset | 3.762 | 0.032 | 3.795 | |
FlowSOMmary | 54.146 | 0.680 | 54.831 | |
GetChannels | 0.023 | 0.000 | 0.023 | |
GetClusterMFIs | 3.694 | 0.011 | 3.707 | |
GetClusters | 3.727 | 0.008 | 3.746 | |
GetCounts | 4.352 | 0.012 | 4.365 | |
GetFeatures | 4.019 | 0.004 | 4.023 | |
GetFlowJoLabels | 6.307 | 0.020 | 6.328 | |
GetMFIs | 3.760 | 0.020 | 3.779 | |
GetMarkers | 0.019 | 0.003 | 0.023 | |
GetMetaclusterCVs | 3.804 | 0.004 | 3.808 | |
GetMetaclusterMFIs | 3.833 | 0.012 | 3.845 | |
GetMetaclusters | 3.699 | 0.004 | 3.704 | |
GetPercentages | 3.648 | 0.004 | 3.653 | |
GroupStats | 14.733 | 0.031 | 14.765 | |
Initialize_KWSP | 0.003 | 0.000 | 0.004 | |
Initialize_PCA | 0.001 | 0.000 | 0.001 | |
MetaClustering | 3.268 | 0.012 | 3.280 | |
MetaclusterCVs | 3.731 | 0.012 | 3.742 | |
MetaclusterMFIs | 3.963 | 0.020 | 3.985 | |
NClusters | 4.117 | 0.008 | 4.126 | |
NMetaclusters | 4.272 | 0.020 | 4.292 | |
NewData | 3.380 | 0.000 | 3.381 | |
Plot2DScatters | 6.402 | 0.032 | 6.434 | |
PlotCenters | 1.239 | 0.008 | 1.247 | |
PlotClusters2D | 0.877 | 0.004 | 0.881 | |
PlotDimRed | 42.647 | 0.032 | 42.682 | |
PlotFileScatters | 0.605 | 0.000 | 0.605 | |
PlotFlowSOM | 7.108 | 0.008 | 7.116 | |
PlotGroups | 13.949 | 0.032 | 13.982 | |
PlotLabels | 4.703 | 0.012 | 4.715 | |
PlotManualBars | 6.699 | 0.014 | 6.713 | |
PlotMarker | 20.789 | 0.044 | 20.837 | |
PlotNode | 7.346 | 0.020 | 7.367 | |
PlotNumbers | 6.816 | 0.004 | 6.821 | |
PlotOverview2D | 3.889 | 0.012 | 3.901 | |
PlotPies | 6.192 | 0.011 | 6.204 | |
PlotSD | 1.938 | 0.008 | 1.946 | |
PlotStars | 7.515 | 0.012 | 7.527 | |
PlotVariable | 4.602 | 0.007 | 4.610 | |
Purity | 0.001 | 0.000 | 0.001 | |
QueryMultiple | 8.232 | 0.012 | 8.245 | |
QueryStarPlot | 6.777 | 0.004 | 6.781 | |
ReadInput | 3.172 | 0.012 | 3.185 | |
ReassignMetaclusters | 14.062 | 0.020 | 14.083 | |
RelabelMetaclusters | 19.939 | 0.028 | 19.969 | |
SaveClustersToFCS | 4.482 | 0.007 | 4.490 | |
TestOutliers | 4.849 | 0.012 | 4.864 | |
UpdateNodeSize | 7.560 | 0.012 | 7.572 | |
get_channels | 0.037 | 0.000 | 0.036 | |
get_markers | 0.022 | 0.001 | 0.023 | |
metaClustering_consensus | 2.630 | 0.006 | 2.636 | |
plotStarLegend | 0.311 | 0.000 | 0.311 | |
print.FlowSOM | 3.552 | 0.012 | 3.564 | |
query_multiple | 8.425 | 0.008 | 8.436 | |