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CHECK report for FlowSOM on malbec1

This page was generated on 2021-05-05 12:09:51 -0400 (Wed, 05 May 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  (landing page)
Sofie Van Gassen
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/FlowSOM
Branch: RELEASE_3_12
Last Commit: 89cd5ba
Last Changed Date: 2020-10-27 11:01:34 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 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: 2021-05-05 01:39:29 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 01:43:15 -0400 (Wed, 05 May 2021)
EllapsedTime: 226.0 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 4.0.5 (2021-03-31)
* 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     13.040  0.152  13.250
FlowSOM          9.996  0.032  10.039
PlotOverview2D   8.136  0.040   8.189
MetaclusterMFIs  5.492  0.004   5.507
* 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
AggregateFlowFrames0.1680.0200.199
BuildMST1.9640.0241.993
BuildSOM1.9240.0081.939
CountGroups13.040 0.15213.250
FMeasure0.0000.0000.003
FlowSOM 9.996 0.03210.039
FlowSOMSubset4.7760.0404.843
GetClusters4.0280.0124.042
GetFlowJoLabels4.2720.0284.416
GetMFIs4.4880.0124.510
GetMetaclusters4.5760.0124.594
Initialize_KWSP0.0040.0000.004
Initialize_PCA0.0000.0000.001
MetaClustering3.4400.0203.472
MetaclusterCVs4.0640.0164.083
MetaclusterMFIs5.4920.0045.507
NewData3.3880.0043.394
PlotCenters1.7920.0001.796
PlotClusters2D1.1280.0001.129
PlotGroups000
PlotLabels3.3800.0043.382
PlotMarker0.9120.0000.914
PlotNode4.1000.0244.127
PlotNumbers1.5360.0041.539
PlotOverview2D8.1360.0408.189
PlotPies4.1480.0004.157
PlotSD1.6080.0001.618
PlotStars1.0760.0161.093
PlotVariable1.2960.0001.309
Purity0.0000.0000.002
QueryStarPlot3.4160.0083.434
ReadInput4.7000.0404.744
TestOutliers4.6520.0044.664
UpdateNodeSize1.1480.0081.155
get_channels0.0200.0040.024
get_markers0.0240.0040.025
metaClustering_consensus2.9040.0122.922