Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:02:58 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 2.12.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings FlowSOM_2.12.0.tar.gz |
StartedAt: 2024-05-31 03:49:47 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 03:58:55 -0400 (Fri, 31 May 2024) |
EllapsedTime: 548.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FlowSOM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --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 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 47.912 0.482 48.062 PlotDimRed 43.640 0.092 43.648 PlotMarker 16.228 0.048 16.277 UpdateMetaclusters 15.739 0.048 15.787 PlotOutliers 15.027 0.016 15.043 PlotStars 13.737 0.044 13.782 GroupStats 11.373 0.028 11.401 FlowSOM 10.648 0.124 10.772 PlotGroups 10.532 0.056 10.589 query_multiple 8.303 0.004 8.306 AddAnnotation 7.907 0.188 8.097 QueryMultiple 8.079 0.008 8.087 GetFlowJoLabels 7.546 0.061 7.607 Plot2DScatters 7.367 0.044 7.381 PlotManualBars 6.494 0.012 6.507 PlotNode 6.395 0.012 6.407 QueryStarPlot 6.084 0.072 6.156 PlotVariable 6.098 0.012 6.109 PlotNumbers 5.823 0.064 5.888 PlotPies 5.671 0.016 5.687 PlotFlowSOM 5.476 0.044 5.520 CountGroups 5.211 0.112 5.323 UpdateNodeSize 5.260 0.004 5.263 NMetaclusters 5.093 0.016 5.109 MetaclusterMFIs 5.091 0.012 5.103 * 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-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.
FlowSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL FlowSOM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘FlowSOM’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c som.c -o som.o gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-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 | 7.907 | 0.188 | 8.097 | |
AggregateFlowFrames | 0.070 | 0.008 | 0.078 | |
BuildMST | 1.104 | 0.012 | 1.116 | |
BuildSOM | 1.278 | 0.040 | 1.318 | |
CountGroups | 5.211 | 0.112 | 5.323 | |
FMeasure | 0.002 | 0.000 | 0.002 | |
FlowSOM | 10.648 | 0.124 | 10.772 | |
FlowSOMSubset | 3.639 | 0.032 | 3.671 | |
FlowSOMmary | 47.912 | 0.482 | 48.062 | |
GetChannels | 0.024 | 0.004 | 0.028 | |
GetClusterMFIs | 3.650 | 0.060 | 3.711 | |
GetClusterPercentagesPositive | 3.774 | 0.040 | 3.815 | |
GetClusters | 3.596 | 0.008 | 3.605 | |
GetCounts | 3.734 | 0.008 | 3.742 | |
GetFeatures | 4.864 | 0.027 | 4.893 | |
GetFlowJoLabels | 7.546 | 0.061 | 7.607 | |
GetMFIs | 4.051 | 0.020 | 4.071 | |
GetMarkers | 0.027 | 0.000 | 0.027 | |
GetMetaclusterCVs | 4.253 | 0.076 | 4.329 | |
GetMetaclusterMFIs | 4.087 | 0.004 | 4.092 | |
GetMetaclusterPercentagesPositive | 4.072 | 0.012 | 4.083 | |
GetMetaclusters | 3.991 | 0.076 | 4.066 | |
GetPercentages | 4.022 | 0.008 | 4.030 | |
GroupStats | 11.373 | 0.028 | 11.401 | |
Initialize_KWSP | 0.003 | 0.000 | 0.004 | |
Initialize_PCA | 0.001 | 0.000 | 0.001 | |
MetaClustering | 2.884 | 0.036 | 2.920 | |
MetaclusterCVs | 4.210 | 0.016 | 4.227 | |
MetaclusterMFIs | 5.091 | 0.012 | 5.103 | |
NClusters | 4.756 | 0.056 | 4.812 | |
NMetaclusters | 5.093 | 0.016 | 5.109 | |
NewData | 3.562 | 0.008 | 3.570 | |
Plot2DScatters | 7.367 | 0.044 | 7.381 | |
PlotCenters | 0.978 | 0.032 | 1.010 | |
PlotClusters2D | 0.935 | 0.008 | 0.944 | |
PlotDimRed | 43.640 | 0.092 | 43.648 | |
PlotFileScatters | 0.754 | 0.011 | 0.766 | |
PlotFlowSOM | 5.476 | 0.044 | 5.520 | |
PlotGroups | 10.532 | 0.056 | 10.589 | |
PlotLabels | 4.878 | 0.024 | 4.902 | |
PlotManualBars | 6.494 | 0.012 | 6.507 | |
PlotMarker | 16.228 | 0.048 | 16.277 | |
PlotNode | 6.395 | 0.012 | 6.407 | |
PlotNumbers | 5.823 | 0.064 | 5.888 | |
PlotOutliers | 15.027 | 0.016 | 15.043 | |
PlotOverview2D | 4.174 | 0.044 | 4.218 | |
PlotPies | 5.671 | 0.016 | 5.687 | |
PlotSD | 1.900 | 0.011 | 1.911 | |
PlotStars | 13.737 | 0.044 | 13.782 | |
PlotVariable | 6.098 | 0.012 | 6.109 | |
Purity | 0.001 | 0.000 | 0.001 | |
QueryMultiple | 8.079 | 0.008 | 8.087 | |
QueryStarPlot | 6.084 | 0.072 | 6.156 | |
ReadInput | 3.101 | 0.008 | 3.115 | |
SaveClustersToFCS | 4.930 | 0.012 | 4.943 | |
TestOutliers | 4.357 | 0.004 | 4.361 | |
UpdateMetaclusters | 15.739 | 0.048 | 15.787 | |
UpdateNodeSize | 5.260 | 0.004 | 5.263 | |
get_channels | 0.027 | 0.004 | 0.031 | |
get_markers | 0.029 | 0.000 | 0.029 | |
metaClustering_consensus | 2.380 | 0.028 | 2.408 | |
plotStarLegend | 0.383 | 0.000 | 0.383 | |
print.FlowSOM | 4.008 | 0.020 | 4.028 | |
query_multiple | 8.303 | 0.004 | 8.306 | |