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CHECK report for FlowSOM on nebbiolo1

This page was generated on 2021-01-19 11:53:29 -0500 (Tue, 19 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE FlowSOM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 631/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 1.22.0
Sofie Van Gassen
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/FlowSOM
Branch: RELEASE_3_12
Last Commit: 89cd5ba
Last Changed Date: 2020-10-27 11:01:34 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: FlowSOM
Version: 1.22.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings FlowSOM_1.22.0.tar.gz
StartedAt: 2021-01-18 21:27:08 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 21:30:53 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 224.4 seconds
RetCode: 0
Status:  OK 
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings FlowSOM_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/FlowSOM.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.22.0’
* 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 ... NOTE
AddFlowFrame: no visible global function definition for ‘is’
ReadInput: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
CountGroups     10.566  0.099  10.766
PlotOverview2D   8.687  0.056   8.769
FlowSOM          8.315  0.060   8.404
TestOutliers     5.564  0.004   5.721
MetaclusterMFIs  5.210  0.016   5.226
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.



Installation output

FlowSOM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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
AggregateFlowFrames0.1420.0080.161
BuildMST1.5150.0281.549
BuildSOM1.3830.0001.384
CountGroups10.566 0.09910.766
FMeasure0.0020.0000.002
FlowSOM8.3150.0608.404
FlowSOMSubset4.0060.0444.064
GetClusters3.9890.0204.035
GetFlowJoLabels4.5460.0364.583
GetMFIs4.4700.0394.510
GetMetaclusters3.9220.0313.989
Initialize_KWSP0.0050.0000.005
Initialize_PCA0.0020.0000.002
MetaClustering3.7810.0083.842
MetaclusterCVs4.1460.0204.180
MetaclusterMFIs5.2100.0165.226
NewData3.7400.0163.794
PlotCenters1.4600.0231.499
PlotClusters2D1.1170.0111.158
PlotGroups0.0000.0010.001
PlotLabels4.3680.0144.428
PlotMarker1.2760.0051.299
PlotNode4.4060.0554.496
PlotNumbers1.1170.0001.118
PlotOverview2D8.6870.0568.769
PlotPies4.0920.0394.136
PlotSD1.3230.0121.341
PlotStars1.3560.0001.381
PlotVariable1.3670.0161.395
Purity0.0010.0000.002
QueryStarPlot2.7300.0242.754
ReadInput3.1550.0323.232
TestOutliers5.5640.0045.721
UpdateNodeSize1.6440.0081.652
get_channels0.0360.0000.037
get_markers0.0370.0040.041
metaClustering_consensus2.9510.0082.974