Back to Multiple platform build/check report for BioC 3.12
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

CHECK report for FlowSOM on malbec1

This page was generated on 2021-01-19 11:51:49 -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: 2021-01-19 02:26:20 -0500 (Tue, 19 Jan 2021)
EndedAt: 2021-01-19 02:30:06 -0500 (Tue, 19 Jan 2021)
EllapsedTime: 225.3 seconds
RetCode: 0
Status:  OK 
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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     11.628  0.096  11.748
FlowSOM          8.740  0.040   8.792
PlotOverview2D   7.952  0.032   7.994
MetaclusterMFIs  5.400  0.032   5.439
GetFlowJoLabels  4.984  0.044   5.088
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* 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
AggregateFlowFrames0.1760.0160.215
BuildMST1.9200.0241.947
BuildSOM1.7000.0081.709
CountGroups11.628 0.09611.748
FMeasure0.0040.0000.002
FlowSOM8.7400.0408.792
FlowSOMSubset4.3880.0324.430
GetClusters4.3080.0204.331
GetFlowJoLabels4.9840.0445.088
GetMFIs4.6480.0084.667
GetMetaclusters4.4960.0364.540
Initialize_KWSP0.0040.0000.003
Initialize_PCA0.0000.0000.001
MetaClustering3.4240.0083.432
MetaclusterCVs4.5200.0084.538
MetaclusterMFIs5.4000.0325.439
NewData3.6560.0243.682
PlotCenters1.5600.0081.568
PlotClusters2D1.9160.0001.932
PlotGroups000
PlotLabels4.5080.0124.550
PlotMarker1.4760.0041.478
PlotNode4.5040.0084.523
PlotNumbers1.1840.0001.187
PlotOverview2D7.9520.0327.994
PlotPies4.3840.0364.437
PlotSD1.3520.0081.358
PlotStars1.2960.0121.309
PlotVariable1.2520.0081.262
Purity0.0040.0000.001
QueryStarPlot3.0440.0123.059
ReadInput3.9240.0164.623
TestOutliers4.8120.0284.845
UpdateNodeSize1.3480.0081.357
get_channels0.0320.0000.033
get_markers0.0200.0040.027
metaClustering_consensus3.1200.0083.129