Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:05:09 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for FlowSOM on nebbiolo2


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.

raw results

Package 670/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.2.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: RELEASE_3_14
git_last_commit: 44e9c9b
git_last_commit_date: 2021-10-26 12:18:07 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FlowSOM
Version: 2.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings FlowSOM_2.2.0.tar.gz
StartedAt: 2022-01-20 07:33:23 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 07:43:18 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 595.1 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings FlowSOM_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.2.0’
* 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        70.195  0.404  70.603
PlotDimRed         52.440  0.020  52.461
PlotMarker         26.904  0.120  27.024
UpdateMetaclusters 24.987  0.028  25.017
PlotGroups         21.606  0.068  21.675
FlowSOM            16.258  0.103  16.362
GroupStats         16.060  0.040  16.104
AddAnnotation      13.016  0.311  13.329
QueryStarPlot      11.197  0.028  11.225
QueryMultiple      10.156  0.008  10.164
query_multiple      9.813  0.024   9.837
PlotPies            9.318  0.024   9.343
PlotManualBars      9.166  0.086   9.253
PlotFlowSOM         8.993  0.020   9.013
PlotStars           8.926  0.008   8.934
PlotNumbers         8.834  0.032   8.866
PlotNode            8.659  0.024   8.684
UpdateNodeSize      8.412  0.020   8.432
Plot2DScatters      8.100  0.024   8.125
PlotLabels          7.357  0.124   7.481
TestOutliers        7.406  0.012   7.419
GetFlowJoLabels     6.606  0.036   6.643
FlowSOMSubset       5.986  0.383   6.371
PlotOverview2D      6.115  0.004   6.118
CountGroups         5.774  0.120   5.894
PlotVariable        5.607  0.024   5.630
SaveClustersToFCS   5.581  0.036   5.617
GetCounts           5.251  0.004   5.256
GetClusterMFIs      5.173  0.036   5.209
* 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-3.14-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.



Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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)

Tests output


Example timings

FlowSOM.Rcheck/FlowSOM-Ex.timings

nameusersystemelapsed
AddAnnotation13.016 0.31113.329
AggregateFlowFrames0.0700.0080.079
BuildMST1.0300.0161.046
BuildSOM1.3830.0041.387
CountGroups5.7740.1205.894
FMeasure0.0020.0000.001
FlowSOM16.258 0.10316.362
FlowSOMSubset5.9860.3836.371
FlowSOMmary70.195 0.40470.603
GetChannels0.040.000.04
GetClusterMFIs5.1730.0365.209
GetClusters4.6890.0324.721
GetCounts5.2510.0045.256
GetFeatures4.8850.0164.904
GetFlowJoLabels6.6060.0366.643
GetMFIs4.1890.0164.205
GetMarkers0.0360.0000.037
GetMetaclusterCVs4.4540.0164.470
GetMetaclusterMFIs4.7920.0124.804
GetMetaclusters3.9420.0203.962
GetPercentages3.8440.0203.865
GroupStats16.060 0.04016.104
Initialize_KWSP0.0060.0000.006
Initialize_PCA000
MetaClustering3.1950.0283.223
MetaclusterCVs4.2890.0244.313
MetaclusterMFIs4.8870.0404.927
NClusters4.4080.0044.411
NMetaclusters4.7680.0244.792
NewData3.2640.0043.268
Plot2DScatters8.1000.0248.125
PlotCenters0.9940.0040.997
PlotClusters2D0.9370.0080.945
PlotDimRed52.440 0.02052.461
PlotFileScatters0.8610.0040.865
PlotFlowSOM8.9930.0209.013
PlotGroups21.606 0.06821.675
PlotLabels7.3570.1247.481
PlotManualBars9.1660.0869.253
PlotMarker26.904 0.12027.024
PlotNode8.6590.0248.684
PlotNumbers8.8340.0328.866
PlotOverview2D6.1150.0046.118
PlotPies9.3180.0249.343
PlotSD2.0620.0082.070
PlotStars8.9260.0088.934
PlotVariable5.6070.0245.630
Purity0.0010.0000.001
QueryMultiple10.156 0.00810.164
QueryStarPlot11.197 0.02811.225
ReadInput3.7240.0323.757
SaveClustersToFCS5.5810.0365.617
TestOutliers7.4060.0127.419
UpdateMetaclusters24.987 0.02825.017
UpdateNodeSize8.4120.0208.432
get_channels0.0240.0000.023
get_markers0.0180.0080.025
metaClustering_consensus2.7530.0202.773
plotStarLegend0.3210.0000.321
print.FlowSOM4.1220.0284.150
query_multiple9.8130.0249.837