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This page was generated on 2021-07-24 12:05:26 -0400 (Sat, 24 Jul 2021).

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 647/2008HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.1.24  (landing page)
Sofie Van Gassen
Snapshot Date: 2021-07-23 14:50:08 -0400 (Fri, 23 Jul 2021)
URL: https://git.bioconductor.org/packages/FlowSOM
Branch: master
Last Commit: aa491e2
Last Changed Date: 2021-07-02 09:32:36 -0400 (Fri, 02 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  NO, package depends on 'flowWorkspace' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: FlowSOM
Version: 2.1.24
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_2.1.24.tar.gz
StartedAt: 2021-07-23 19:43:58 -0400 (Fri, 23 Jul 2021)
EndedAt: 2021-07-23 19:51:40 -0400 (Fri, 23 Jul 2021)
EllapsedTime: 461.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: FlowSOM.Rcheck
Warnings: 1

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_2.1.24.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/FlowSOM.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* 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 ‘2.1.24’
* 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 ... WARNING
Undocumented code objects:
  ‘UpdateMetaclusters’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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     54.021  0.156  54.179
PlotDimRed      41.286  0.016  41.303
PlotMarker      21.382  0.052  21.436
FlowSOM         13.917  0.531  14.450
GroupStats      14.315  0.024  14.339
PlotGroups      12.353  0.064  12.417
AddAnnotation    9.709  0.183   9.893
QueryMultiple    9.475  0.016   9.491
PlotStars        8.290  0.084   8.375
PlotNode         8.331  0.020   8.352
query_multiple   8.242  0.016   8.258
PlotPies         7.742  0.020   7.762
QueryStarPlot    7.331  0.016   7.348
UpdateNodeSize   7.178  0.020   7.198
PlotNumbers      7.130  0.028   7.158
PlotFlowSOM      7.002  0.012   7.013
Plot2DScatters   6.650  0.028   6.678
GetFlowJoLabels  6.372  0.012   6.384
PlotManualBars   6.266  0.032   6.299
PlotVariable     5.476  0.016   5.493
PlotLabels       5.252  0.008   5.260
CountGroups      5.107  0.072   5.178
* 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 WARNING, 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
###
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* 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
AddAnnotation9.7090.1839.893
AggregateFlowFrames0.0620.0070.070
BuildMST0.9090.0120.922
BuildSOM0.9530.0080.961
CountGroups5.1070.0725.178
FMeasure0.0020.0000.001
FlowSOM13.917 0.53114.450
FlowSOMSubset4.7450.1444.889
FlowSOMmary54.021 0.15654.179
GetChannels0.0210.0000.021
GetClusterMFIs3.7670.0043.771
GetClusters3.6880.0083.696
GetCounts3.7430.0163.759
GetFeatures3.7830.0123.795
GetFlowJoLabels6.3720.0126.384
GetMFIs3.7560.0083.765
GetMarkers0.0210.0000.021
GetMetaclusterCVs3.6730.0123.686
GetMetaclusterMFIs3.7260.0083.734
GetMetaclusters3.7390.0083.748
GetPercentages3.7790.0083.787
GroupStats14.315 0.02414.339
Initialize_KWSP0.0040.0000.004
Initialize_PCA0.0010.0000.001
MetaClustering2.8890.0202.909
MetaclusterCVs3.9810.0003.981
MetaclusterMFIs4.7890.0124.802
NClusters4.4410.0124.453
NMetaclusters4.5870.0084.595
NewData3.8880.0243.912
Plot2DScatters6.6500.0286.678
PlotCenters0.8830.0040.888
PlotClusters2D0.8780.0120.890
PlotDimRed41.286 0.01641.303
PlotFileScatters0.5980.0000.598
PlotFlowSOM7.0020.0127.013
PlotGroups12.353 0.06412.417
PlotLabels5.2520.0085.260
PlotManualBars6.2660.0326.299
PlotMarker21.382 0.05221.436
PlotNode8.3310.0208.352
PlotNumbers7.1300.0287.158
PlotOverview2D4.5220.0724.595
PlotPies7.7420.0207.762
PlotSD1.9730.0161.990
PlotStars8.2900.0848.375
PlotVariable5.4760.0165.493
Purity0.0010.0000.001
QueryMultiple9.4750.0169.491
QueryStarPlot7.3310.0167.348
ReadInput2.5640.0332.597
SaveClustersToFCS4.1400.0314.171
TestOutliers4.7760.0044.780
UpdateNodeSize7.1780.0207.198
get_channels0.0230.0000.024
get_markers0.0290.0030.033
metaClustering_consensus2.1460.0202.166
plotStarLegend0.3040.0000.304
print.FlowSOM3.4790.0163.495
query_multiple8.2420.0168.258